diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
index a3570d33240529319f1539e9b8a66c8b6f5634b5..159598e7dc0ec8a81d954774990dc5ea46a51102 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.cdplugin.copypaste;
+import org.apache.log4j.Logger;
+
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
@@ -9,8 +11,6 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.common.SystemClipboard;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import org.apache.log4j.Logger;
-
/**
* CD Plugin action resposible for translating annotation stored in notes to xml
* format stored in annotations.
@@ -19,72 +19,72 @@ import org.apache.log4j.Logger;
*
*/
public class CopyAction extends CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(CopyAction.class.getName());
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(CopyAction.class.getName());
- /**
- * Method that perform annotation of a celldesigner species listed in
- * speciesList.
- *
- * @param plug
- * - a plugin object
- * @param speciesList
- * - list of species to annotate
- * @param win
- * - main window of cell designer
- */
- public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
+ /**
+ * Method that perform annotation of a celldesigner species listed in
+ * speciesList.
+ *
+ * @param plug
+ * - a plugin object
+ * @param speciesList
+ * - list of species to annotate
+ * @param win
+ * - main window of cell designer
+ */
+ public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
- // if list is empty then just return from the method
- if (speciesList.size() == 0) {
- return;
- }
+ // if list is empty then just return from the method
+ if (speciesList.size() == 0) {
+ return;
+ }
- SystemClipboard sc = new SystemClipboard();
+ SystemClipboard sc = new SystemClipboard();
- this.setWindow(win);
- this.setPlug(plug);
+ this.setWindow(win);
+ this.setPlug(plug);
- int size = speciesList.size();
+ int size = speciesList.size();
- PluginSBase chosenElement = null;
- String id = "";
- for (int i = 0; i < size; i++) {
- PluginSBase element = speciesList.get(i);
- if (element instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
- PluginSpecies species = alias.getSpecies();
+ PluginSBase chosenElement = null;
+ String id = "";
+ for (int i = 0; i < size; i++) {
+ PluginSBase element = speciesList.get(i);
+ if (element instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
+ PluginSpecies species = alias.getSpecies();
- if (chosenElement == null) {
- chosenElement = species;
- id = species.getId();
- } else if (id.compareTo(species.getId()) < 0) {
- chosenElement = species;
- id = species.getId();
- }
- } else if (element instanceof PluginReaction) {
- PluginReaction reaction = (PluginReaction) element;
- if (chosenElement == null) {
- chosenElement = reaction;
- id = reaction.getId();
- } else if (id.compareTo(reaction.getId()) < 0) {
- chosenElement = reaction;
- id = reaction.getId();
- }
- } else {
- logger.warn("Unknown class type :" + element.getClass());
- }
- }
+ if (chosenElement == null) {
+ chosenElement = species;
+ id = species.getId();
+ } else if (id.compareTo(species.getId()) < 0) {
+ chosenElement = species;
+ id = species.getId();
+ }
+ } else if (element instanceof PluginReaction) {
+ PluginReaction reaction = (PluginReaction) element;
+ if (chosenElement == null) {
+ chosenElement = reaction;
+ id = reaction.getId();
+ } else if (id.compareTo(reaction.getId()) < 0) {
+ chosenElement = reaction;
+ id = reaction.getId();
+ }
+ } else {
+ logger.warn("Unknown class type :" + element.getClass());
+ }
+ }
- if (chosenElement != null) {
- try {
- sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
- } catch (InvalidXmlSchemaException e) {
- logger.warn("Problem with creating copy-paste String", e);
- }
- }
- }
+ if (chosenElement != null) {
+ try {
+ sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
+ } catch (InvalidXmlSchemaException e) {
+ logger.warn("Problem with creating copy-paste String", e);
+ }
+ }
+ }
}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
index 74f7b881175730d43942abdc186190e76d54790e..04180351ed7c37888c681aa912193a44c0fd4fac 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
@@ -7,7 +7,6 @@ import org.apache.log4j.Logger;
import jp.sbi.celldesigner.MainWindow;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
@@ -22,165 +21,166 @@ import lcsb.mapviewer.model.map.MiriamType;
*
*/
public class CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(CopyPasteAbstractAction.class);
-
- /**
- * Prefix used for serialization/deserialization of {@link MiriamData} to
- * string stored in system clipboard.
- */
- private static final String PREFIX = "[MIRIAM]";
- /**
- * Plugin object which ran this action. This object is used to update
- * information about species
- */
- private CopyPastePlugin plug;
- /**
- * Object of CellDesigner main form.
- */
- private MainWindow window;
-
- /**
- * Serializes {@link MiriamData} into string that will be stored into system
- * clipboard.
- *
- * @param md
- * object to serialize
- * @return string representation of {@link MiriamData}
- */
- protected String serialize(MiriamData md) {
- return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0) + "\t" + md.getResource();
- }
-
- /**
- * Deserialize {@link MiriamData} from string creted by
- * {@link #serialize(MiriamData)} method.
- *
- * @param string
- * string representation of {@link MiriamData}
- * @return {@link MiriamData} obtained from input string
- */
- protected MiriamData deserialize(String string) {
- if (string == null) {
- return null;
- }
- String[] tmp = string.split("\t");
-
- // CHECKSTYLE:OFF
- if (tmp.length == 4) {
- if (PREFIX.equals(tmp[0])) {
- String relation = tmp[1];
- String uri = tmp[2];
- String resource = tmp[3];
- MiriamType mt = MiriamType.getTypeByUri(uri);
- MiriamRelationType mrt = MiriamRelationType.getTypeByStringRepresentation(relation);
- if (mt == null || mrt == null) {
- return null;
- }
- return new MiriamData(mrt, mt, resource);
- }
- }
- // CHECKSTYLE:ON
- return null;
- }
-
- /**
- * Returns serialized string of annotations and notes.
- *
- * @param annotationString
- * xml string representing annotations in CellDesigner
- * @param notesString
- * flat notes String
- * @return serialized string
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
- XmlAnnotationParser xap = new XmlAnnotationParser();
- Set<MiriamData> set = xap.parse(annotationString);
- StringBuilder result = new StringBuilder();
- for (MiriamData md : set) {
- result.append(serialize(md) + "\n");
- }
- result.append(notesString);
- return result.toString();
- }
-
- /**
- * Deserialize string created by {@link #getCopyString(String, String)}
- * method. Used to create {@link MiriamData} set and notes from clipboard.
- *
- * @param value
- * string for deserialization
- *
- * @return {@link Pair} of {@link MiriamData} set and notes string
- */
- protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
- if (value == null) {
- return new Pair<Set<MiriamData>, String>(null, null);
- }
- String[] rows = value.split("\n");
-
- StringBuilder sb = new StringBuilder("");
-
- boolean miriam = true;
-
- Set<MiriamData> set = new HashSet<MiriamData>();
- for (int i = 0; i < rows.length; i++) {
- String row = rows[i];
- if (miriam) {
- MiriamData md = deserialize(row);
- if (md != null) {
- set.add(md);
- } else {
- miriam = false;
- }
- }
- if (!miriam) {
- sb.append(row);
- sb.append("\n");
- }
- }
- String notes = sb.toString().trim();
-
- return new Pair<Set<MiriamData>, String>(set, notes);
- }
-
- /**
- * @return the plug
- * @see #plug
- */
- protected CopyPastePlugin getPlug() {
- return plug;
- }
-
- /**
- * @param plug
- * the plug to set
- * @see #plug
- */
- protected void setPlug(CopyPastePlugin plug) {
- this.plug = plug;
- }
-
- /**
- * @return the window
- * @see #window
- */
- protected MainWindow getWindow() {
- return window;
- }
-
- /**
- * @param window
- * the window to set
- * @see #window
- */
- protected void setWindow(MainWindow window) {
- this.window = window;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(CopyPasteAbstractAction.class);
+
+ /**
+ * Prefix used for serialization/deserialization of {@link MiriamData} to string
+ * stored in system clipboard.
+ */
+ private static final String PREFIX = "[MIRIAM]";
+ /**
+ * Plugin object which ran this action. This object is used to update
+ * information about species
+ */
+ private CopyPastePlugin plug;
+ /**
+ * Object of CellDesigner main form.
+ */
+ private MainWindow window;
+
+ /**
+ * Serializes {@link MiriamData} into string that will be stored into system
+ * clipboard.
+ *
+ * @param md
+ * object to serialize
+ * @return string representation of {@link MiriamData}
+ */
+ protected String serialize(MiriamData md) {
+ return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0)
+ + "\t" + md.getResource();
+ }
+
+ /**
+ * Deserialize {@link MiriamData} from string creted by
+ * {@link #serialize(MiriamData)} method.
+ *
+ * @param string
+ * string representation of {@link MiriamData}
+ * @return {@link MiriamData} obtained from input string
+ */
+ protected MiriamData deserialize(String string) {
+ if (string == null) {
+ return null;
+ }
+ String[] tmp = string.split("\t");
+
+ // CHECKSTYLE:OFF
+ if (tmp.length == 4) {
+ if (PREFIX.equals(tmp[0])) {
+ String relation = tmp[1];
+ String uri = tmp[2];
+ String resource = tmp[3];
+ MiriamType mt = MiriamType.getTypeByUri(uri);
+ MiriamRelationType mrt = MiriamRelationType.getTypeByStringRepresentation(relation);
+ if (mt == null || mrt == null) {
+ return null;
+ }
+ return new MiriamData(mrt, mt, resource);
+ }
+ }
+ // CHECKSTYLE:ON
+ return null;
+ }
+
+ /**
+ * Returns serialized string of annotations and notes.
+ *
+ * @param annotationString
+ * xml string representing annotations in CellDesigner
+ * @param notesString
+ * flat notes String
+ * @return serialized string
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
+ XmlAnnotationParser xap = new XmlAnnotationParser();
+ Set<MiriamData> set = xap.parse(annotationString);
+ StringBuilder result = new StringBuilder();
+ for (MiriamData md : set) {
+ result.append(serialize(md) + "\n");
+ }
+ result.append(notesString);
+ return result.toString();
+ }
+
+ /**
+ * Deserialize string created by {@link #getCopyString(String, String)} method.
+ * Used to create {@link MiriamData} set and notes from clipboard.
+ *
+ * @param value
+ * string for deserialization
+ *
+ * @return {@link Pair} of {@link MiriamData} set and notes string
+ */
+ protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
+ if (value == null) {
+ return new Pair<Set<MiriamData>, String>(null, null);
+ }
+ String[] rows = value.split("\n");
+
+ StringBuilder sb = new StringBuilder("");
+
+ boolean miriam = true;
+
+ Set<MiriamData> set = new HashSet<MiriamData>();
+ for (int i = 0; i < rows.length; i++) {
+ String row = rows[i];
+ if (miriam) {
+ MiriamData md = deserialize(row);
+ if (md != null) {
+ set.add(md);
+ } else {
+ miriam = false;
+ }
+ }
+ if (!miriam) {
+ sb.append(row);
+ sb.append("\n");
+ }
+ }
+ String notes = sb.toString().trim();
+
+ return new Pair<Set<MiriamData>, String>(set, notes);
+ }
+
+ /**
+ * @return the plug
+ * @see #plug
+ */
+ protected CopyPastePlugin getPlug() {
+ return plug;
+ }
+
+ /**
+ * @param plug
+ * the plug to set
+ * @see #plug
+ */
+ protected void setPlug(CopyPastePlugin plug) {
+ this.plug = plug;
+ }
+
+ /**
+ * @return the window
+ * @see #window
+ */
+ protected MainWindow getWindow() {
+ return window;
+ }
+
+ /**
+ * @param window
+ * the window to set
+ * @see #window
+ */
+ protected void setWindow(MainWindow window) {
+ this.window = window;
+ }
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
index 17bdd87eeb291787f641d2036540c93a50130881..c9a139cf0dcf04f5b108477a56569103268e7415 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
@@ -4,12 +4,12 @@ import java.awt.KeyEventDispatcher;
import java.awt.KeyboardFocusManager;
import java.awt.event.KeyEvent;
+import org.apache.log4j.Logger;
+
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
import jp.sbi.celldesigner.plugin.PluginSBase;
-import org.apache.log4j.Logger;
-
/**
* This class represent a plugin to cell designer with copy past functionality
* that allows to copy and paste notes and annotations of species.
@@ -29,103 +29,101 @@ import org.apache.log4j.Logger;
*/
public class CopyPastePlugin extends CellDesignerPlugin {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CopyPastePlugin.class.getName());
- /**
- * Main window of cell designer.
- */
- private MainWindow win;
-
- /**
- * Paste action.
- */
- private PastePluginAction ppa;
-
- /**
- * Paste action.
- */
- private CopyPluginAction cpa;
-
- /**
- * Default constructor. Creates menu and InfoFrame.
- */
- public CopyPastePlugin() {
- try {
- // PropertyConfigurator.configure("D:/log4j.properties");
- logger.debug("Loading copy-paste plugin...");
-
- win = MainWindow.getLastInstance();
-
- ppa = new PastePluginAction(this, win);
- cpa = new CopyPluginAction(this, win);
-
- // create keyboard listener for shortcuts
- KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
- public boolean dispatchKeyEvent(KeyEvent e) {
- switch (e.getID()) {
- case KeyEvent.KEY_PRESSED:
- if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
- && e.isControlDown()
- && e.isAltDown()
- ) {
- ppa.myActionPerformed(null);
- return true;
- } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
- && e.isControlDown()
- && e.isAltDown()
- ) {
- cpa.myActionPerformed(null);
- return true;
- } else {
- return false;
- }
- default:
- return false;
- }
- }
- });
-
- } catch (Exception exception) {
- logger.error(exception, exception);
- }
- }
-
- // CHECKSTYLE:OFF
- @Override
- public void SBaseAdded(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseChanged(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
- // CHECKSTYLE:ON
-
- @Override
- public void addPluginMenu() {
- }
-
- @Override
- public void modelClosed(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelOpened(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelSelectChanged(PluginSBase arg0) {
-
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CopyPastePlugin.class.getName());
+ /**
+ * Main window of cell designer.
+ */
+ private MainWindow win;
+
+ /**
+ * Paste action.
+ */
+ private PastePluginAction ppa;
+
+ /**
+ * Paste action.
+ */
+ private CopyPluginAction cpa;
+
+ /**
+ * Default constructor. Creates menu and InfoFrame.
+ */
+ public CopyPastePlugin() {
+ try {
+ // PropertyConfigurator.configure("D:/log4j.properties");
+ logger.debug("Loading copy-paste plugin...");
+
+ win = MainWindow.getLastInstance();
+
+ ppa = new PastePluginAction(this, win);
+ cpa = new CopyPluginAction(this, win);
+
+ // create keyboard listener for shortcuts
+ KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
+ public boolean dispatchKeyEvent(KeyEvent e) {
+ switch (e.getID()) {
+ case KeyEvent.KEY_PRESSED:
+ if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
+ && e.isControlDown()
+ && e.isAltDown()) {
+ ppa.myActionPerformed(null);
+ return true;
+ } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
+ && e.isControlDown()
+ && e.isAltDown()) {
+ cpa.myActionPerformed(null);
+ return true;
+ } else {
+ return false;
+ }
+ default:
+ return false;
+ }
+ }
+ });
+
+ } catch (Exception exception) {
+ logger.error(exception, exception);
+ }
+ }
+
+ // CHECKSTYLE:OFF
+ @Override
+ public void SBaseAdded(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseChanged(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseDeleted(PluginSBase arg0) {
+ }
+
+ // CHECKSTYLE:ON
+
+ @Override
+ public void addPluginMenu() {
+ }
+
+ @Override
+ public void modelClosed(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelOpened(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelSelectChanged(PluginSBase arg0) {
+
+ }
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
index 8fee9aee00c6487125e41c34eefc37552445603a..e38720c08d9be2b9e30496d37822be6173c23e80 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
@@ -2,12 +2,12 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
+import org.apache.log4j.Logger;
+
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
import jp.sbi.celldesigner.plugin.PluginListOf;
-import org.apache.log4j.Logger;
-
/**
* This class represent action that copy species/reaction annotations and notes
* into clipboard.
@@ -17,46 +17,46 @@ import org.apache.log4j.Logger;
*/
public class CopyPluginAction extends PluginAction {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PasteAction.class.getName());
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Plugin that access this action.
- */
- private CopyPastePlugin plug = null;
- /**
- * Main window of CellDesigner.
- */
- private MainWindow window;
-
- /**
- * Default constructor.
- *
- * @param plugin
- * {@link #plug}
- * @param win
- * {@link #window}
- */
- public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
- this.plug = plugin;
- this.window = win;
- }
-
- @Override
- public void myActionPerformed(ActionEvent e) {
- try {
- CopyAction annotateAction = new CopyAction();
- PluginListOf list = plug.getSelectedAllNode();
- annotateAction.performAnnotation(plug, list, window);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PasteAction.class.getName());
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Plugin that access this action.
+ */
+ private CopyPastePlugin plug = null;
+ /**
+ * Main window of CellDesigner.
+ */
+ private MainWindow window;
+
+ /**
+ * Default constructor.
+ *
+ * @param plugin
+ * {@link #plug}
+ * @param win
+ * {@link #window}
+ */
+ public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
+ this.plug = plugin;
+ this.window = win;
+ }
+
+ @Override
+ public void myActionPerformed(ActionEvent e) {
+ try {
+ CopyAction annotateAction = new CopyAction();
+ PluginListOf list = plug.getSelectedAllNode();
+ annotateAction.performAnnotation(plug, list, window);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
index d554598646d7e42956bdd3a68bbd393366a55b9a..4715616172b73217587bd43e2b633560383c7072 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
@@ -23,60 +23,60 @@ import lcsb.mapviewer.model.map.MiriamData;
*
*/
public class PasteAction extends CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(PasteAction.class.getName());
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(PasteAction.class.getName());
- /**
- * Method that perform annotation of a celldesigner species listed in
- * speciesList.
- *
- * @param plug
- * - a plugin object
- * @param speciesList
- * - list of species to annotate
- * @param win
- * - main window of cell designer
- */
- public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
+ /**
+ * Method that perform annotation of a celldesigner species listed in
+ * speciesList.
+ *
+ * @param plug
+ * - a plugin object
+ * @param speciesList
+ * - list of species to annotate
+ * @param win
+ * - main window of cell designer
+ */
+ public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
- XmlAnnotationParser xap = new XmlAnnotationParser();
+ XmlAnnotationParser xap = new XmlAnnotationParser();
- // if list is empty then just return from the method
- if (speciesList.size() == 0) {
- return;
- }
+ // if list is empty then just return from the method
+ if (speciesList.size() == 0) {
+ return;
+ }
- SystemClipboard sc = new SystemClipboard();
- String value = sc.getClipboardContents();
+ SystemClipboard sc = new SystemClipboard();
+ String value = sc.getClipboardContents();
- Pair<Set<MiriamData>, String> data = getAnnotationDataFromClipboardString(value);
- String notes = data.getRight();
- Set<MiriamData> set = data.getLeft();
+ Pair<Set<MiriamData>, String> data = getAnnotationDataFromClipboardString(value);
+ String notes = data.getRight();
+ Set<MiriamData> set = data.getLeft();
- this.setWindow(win);
- this.setPlug(plug);
+ this.setWindow(win);
+ this.setPlug(plug);
- int size = speciesList.size();
- for (int i = 0; i < size; i++) {
- PluginSBase element = speciesList.get(i);
- if (element instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
- PluginSpecies species = alias.getSpecies();
- species.setNotes(notes);
- species.setAnnotationString(xap.dataSetToXmlString(set));
- plug.notifySBaseChanged(element);
- plug.notifySBaseChanged(species);
- } else if (element instanceof PluginReaction) {
- PluginReaction reaction = (PluginReaction) element;
- reaction.setNotes(notes);
- reaction.setAnnotationString(xap.dataSetToXmlString(set));
- plug.notifySBaseChanged(element);
- } else {
- logger.warn("Unknown class type :" + element.getClass());
- }
- }
- }
+ int size = speciesList.size();
+ for (int i = 0; i < size; i++) {
+ PluginSBase element = speciesList.get(i);
+ if (element instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
+ PluginSpecies species = alias.getSpecies();
+ species.setNotes(notes);
+ species.setAnnotationString(xap.dataSetToXmlString(set));
+ plug.notifySBaseChanged(element);
+ plug.notifySBaseChanged(species);
+ } else if (element instanceof PluginReaction) {
+ PluginReaction reaction = (PluginReaction) element;
+ reaction.setNotes(notes);
+ reaction.setAnnotationString(xap.dataSetToXmlString(set));
+ plug.notifySBaseChanged(element);
+ } else {
+ logger.warn("Unknown class type :" + element.getClass());
+ }
+ }
+ }
}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
index 16e44f3ff2d12c1418ff47481cda6a49543fa8bd..0cf65ce58cdaca0a7d5baf548718cf774640533a 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
@@ -2,12 +2,12 @@ package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
+import org.apache.log4j.Logger;
+
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
import jp.sbi.celldesigner.plugin.PluginListOf;
-import org.apache.log4j.Logger;
-
/**
* This class represent action that paste annotations and notes from clipboard
* into selected species/reactions.
@@ -17,45 +17,45 @@ import org.apache.log4j.Logger;
*/
public class PastePluginAction extends PluginAction {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PasteAction.class.getName());
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- /**
- * Plugin that access this action.
- */
- private CopyPastePlugin plug = null;
- /**
- * Main window of CellDesigner.
- */
- private MainWindow window;
-
- /**
- * Default constructor.
- *
- * @param plugin
- * {@link #plug}
- * @param win
- * {@link #window}
- */
- public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
- this.plug = plugin;
- this.window = win;
- }
-
- @Override
- public void myActionPerformed(ActionEvent e) {
- try {
- PasteAction annotateAction = new PasteAction();
- PluginListOf list = plug.getSelectedAllNode();
- annotateAction.performAnnotation(plug, list, window);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PasteAction.class.getName());
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ /**
+ * Plugin that access this action.
+ */
+ private CopyPastePlugin plug = null;
+ /**
+ * Main window of CellDesigner.
+ */
+ private MainWindow window;
+
+ /**
+ * Default constructor.
+ *
+ * @param plugin
+ * {@link #plug}
+ * @param win
+ * {@link #window}
+ */
+ public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
+ this.plug = plugin;
+ this.window = win;
+ }
+
+ @Override
+ public void myActionPerformed(ActionEvent e) {
+ try {
+ PasteAction annotateAction = new PasteAction();
+ PluginListOf list = plug.getSelectedAllNode();
+ annotateAction.performAnnotation(plug, list, window);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
index aea1cfceeaacf72e56d8d0870b5122860cee1247..00a7777f53c9f3757dc730c3edbeb5e4609e3d1f 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
@@ -6,4 +6,3 @@
* {@link lcsb.mapviewer.cdplugin.copypaste.CopyPastePlugin}.
*/
package lcsb.mapviewer.cdplugin.copypaste;
-
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
index f480bc4101a454d9682b6ba439588b98942e5cd1..161cc2f346ae22eea57b323f0671f4255ea49d96 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
@@ -17,10 +17,10 @@ import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-
import org.apache.log4j.Logger;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+
/**
* This class represent a frame that visualise MIRIAM data and notes for a
* species. Only one instance of JFrame is stored in the class (only one window
@@ -31,242 +31,243 @@ import org.apache.log4j.Logger;
*/
public final class InfoFrame {
- /**
- * What should be the distance between description of different aliases.
- */
- private static final int DISTANCE_BETWEEN_PANELS = 5;
-
- /**
- * How many columns should be in the info panel grid.
- */
- private static final int GRID_INFO_COL_NUMBER = 2;
-
- /**
- * How many rows should be in the info panel grid.
- */
- private static final int GRID_INFO_ROW_NUMBER = 3;
-
- /**
- * Frame height.
- */
- private static final int FRAME_HEIGHT = 200;
-
- /**
- * Frame width.
- */
- private static final int FRAME_WIDTH = 200;
-
- /**
- * Font size of the caption label.
- */
- private static final int CAPTION_FONT_SIZE = 18;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(InfoFrame.class.getName());
-
- /**
- * Instance of the JFrame representation of windows.
- */
- private JFrame frame = null;
-
- /**
- * Singleton instance of this class (there can be only one instance of the
- * frame).
- */
- private static InfoFrame instance = null;
-
- /**
- * Font used for captions.
- */
- private Font captionFont = new Font("Default", Font.PLAIN, CAPTION_FONT_SIZE);
-
- /**
- * List of selected aliases.
- */
- private ArrayList<PluginSpeciesAlias> species = new ArrayList<PluginSpeciesAlias>();
-
- /**
- * Default constructor.
- */
- private InfoFrame() {
- int width = FRAME_WIDTH;
- int height = FRAME_HEIGHT;
-
- // check the resolution of the screen
- Toolkit tk = Toolkit.getDefaultToolkit();
- Dimension screenSize = tk.getScreenSize();
- int screenHeight = screenSize.height;
- int screenWidth = screenSize.width;
-
- // if the resultion of the screen changed in a meantime adjust position to
- // be
- // visible on the screen
- width = Math.min(width, screenWidth);
- height = Math.min(height, screenHeight);
-
- int posX = (screenWidth - width) / 2;
- int posY = (screenHeight - height) / 2;
-
- frame = new JFrame("Element information");
- frame.setSize(width, height);
- frame.setLocation(posX, posY);
- frame.setAlwaysOnTop(true);
- frame.setVisible(false);
- }
-
- /**
- * Returns singleton instance of the class.
- *
- * @return singleton instance of this class
- */
- public static InfoFrame getInstance() {
- if (InfoFrame.instance == null) {
- instance = new InfoFrame();
- }
- return instance;
- }
-
- /**
- * Set visible flag for {@link #frame}.
- *
- * @param visible
- * should the frame be visible or not
- */
- public void setVisible(boolean visible) {
- frame.setVisible(visible);
- }
-
- /**
- * This method assign a set of species to this form.
- *
- * @param species
- * - species to be shown in the form
- */
- public void setSpecies(ArrayList<PluginSpeciesAlias> species) {
- this.species = species;
- updateSpecies();
- }
-
- /**
- * Updates information about species in the form.
- */
- protected void updateSpecies() {
- int panels = species.size() + 1;
-
- JPanel controlArea = new JPanel(new GridLayout(panels, 1));
- controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
- // for every species create a panel and add it to general form
- for (PluginSpeciesAlias sp : this.species) {
- JPanel panel = getPanelViewForSpecies(sp);
- controlArea.add(panel);
- }
- // after adding all species add a text area which is "invisible", the main
- // purpose of it is to fill the empty space in the form
- JTextArea text = new JTextArea();
- text.setEditable(false);
- text.setBackground(frame.getBackground());
- controlArea.add(text);
-
- Container content = frame.getContentPane();
- content.removeAll();
-
- // the whole panel should be scrollable
- JScrollPane scrollBar = new JScrollPane(controlArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollBar.setPreferredSize(new Dimension(0, 0));
- content.add(scrollBar);
-
- frame.validate();
- }
-
- /**
- * This method create a panel for a species with all information to be
- * presented.
- *
- * @param species
- * CellDesigner species alias
- * @return {@link JPanel} object with information about species
- */
- private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
- JPanel result = new JPanel();
- result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
-
- // create a caption
- JPanel tmpPanel = new JPanel(new GridLayout(GRID_INFO_ROW_NUMBER, GRID_INFO_COL_NUMBER));
- JLabel label = new JLabel("Element: ", JLabel.RIGHT);
- label.setFont(captionFont);
- tmpPanel.add(label, Component.RIGHT_ALIGNMENT);
- JTextField textField = new JTextField(species.getSpecies().getName(), JLabel.LEFT);
- textField.setFont(captionFont);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- tmpPanel.add(new JLabel("Alias id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
- textField = new JTextField(species.getAliasID(), JLabel.LEFT);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- tmpPanel.add(new JLabel("Species id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
- textField = new JTextField(species.getSpecies().getId(), JLabel.LEFT);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- result.add(tmpPanel);
-
- // add empty space between labels
- result.add(Box.createRigidArea(new Dimension(DISTANCE_BETWEEN_PANELS, DISTANCE_BETWEEN_PANELS)));
-
- return result;
- }
-
- /**
- * Returns info if the frame is visible.
- *
- * @return info if the frame is visible
- */
- public boolean isVisible() {
- return frame.isVisible();
- }
-
- /**
- * Sets frame title.
- *
- * @param title
- * title of the frame
- */
- public void setTitle(String title) {
- frame.setTitle(title);
- }
-
- /**
- * Returns frame title.
- *
- * @return frame title
- */
- public JFrame getFrame() {
- return frame;
- }
-
- /**
- * Set {@link JFrame#defaultCloseOperation}.
- *
- * @param type
- * new {@link JFrame#defaultCloseOperation} value
- */
- public void setDefaultCloseOperation(int type) {
- frame.setDefaultCloseOperation(type);
- }
-
- /**
- * Set {@link JFrame#setAlwaysOnTop(boolean)}.
- *
- * @param always
- * new {@link JFrame#isAlwaysOnTop()} value
- */
- public void setAlwaysOnTop(boolean always) {
- frame.setAlwaysOnTop(always);
- }
+ /**
+ * What should be the distance between description of different aliases.
+ */
+ private static final int DISTANCE_BETWEEN_PANELS = 5;
+
+ /**
+ * How many columns should be in the info panel grid.
+ */
+ private static final int GRID_INFO_COL_NUMBER = 2;
+
+ /**
+ * How many rows should be in the info panel grid.
+ */
+ private static final int GRID_INFO_ROW_NUMBER = 3;
+
+ /**
+ * Frame height.
+ */
+ private static final int FRAME_HEIGHT = 200;
+
+ /**
+ * Frame width.
+ */
+ private static final int FRAME_WIDTH = 200;
+
+ /**
+ * Font size of the caption label.
+ */
+ private static final int CAPTION_FONT_SIZE = 18;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(InfoFrame.class.getName());
+
+ /**
+ * Instance of the JFrame representation of windows.
+ */
+ private JFrame frame = null;
+
+ /**
+ * Singleton instance of this class (there can be only one instance of the
+ * frame).
+ */
+ private static InfoFrame instance = null;
+
+ /**
+ * Font used for captions.
+ */
+ private Font captionFont = new Font("Default", Font.PLAIN, CAPTION_FONT_SIZE);
+
+ /**
+ * List of selected aliases.
+ */
+ private ArrayList<PluginSpeciesAlias> species = new ArrayList<PluginSpeciesAlias>();
+
+ /**
+ * Default constructor.
+ */
+ private InfoFrame() {
+ int width = FRAME_WIDTH;
+ int height = FRAME_HEIGHT;
+
+ // check the resolution of the screen
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ Dimension screenSize = tk.getScreenSize();
+ int screenHeight = screenSize.height;
+ int screenWidth = screenSize.width;
+
+ // if the resultion of the screen changed in a meantime adjust position to
+ // be
+ // visible on the screen
+ width = Math.min(width, screenWidth);
+ height = Math.min(height, screenHeight);
+
+ int posX = (screenWidth - width) / 2;
+ int posY = (screenHeight - height) / 2;
+
+ frame = new JFrame("Element information");
+ frame.setSize(width, height);
+ frame.setLocation(posX, posY);
+ frame.setAlwaysOnTop(true);
+ frame.setVisible(false);
+ }
+
+ /**
+ * Returns singleton instance of the class.
+ *
+ * @return singleton instance of this class
+ */
+ public static InfoFrame getInstance() {
+ if (InfoFrame.instance == null) {
+ instance = new InfoFrame();
+ }
+ return instance;
+ }
+
+ /**
+ * Set visible flag for {@link #frame}.
+ *
+ * @param visible
+ * should the frame be visible or not
+ */
+ public void setVisible(boolean visible) {
+ frame.setVisible(visible);
+ }
+
+ /**
+ * This method assign a set of species to this form.
+ *
+ * @param species
+ * - species to be shown in the form
+ */
+ public void setSpecies(ArrayList<PluginSpeciesAlias> species) {
+ this.species = species;
+ updateSpecies();
+ }
+
+ /**
+ * Updates information about species in the form.
+ */
+ protected void updateSpecies() {
+ int panels = species.size() + 1;
+
+ JPanel controlArea = new JPanel(new GridLayout(panels, 1));
+ controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
+ // for every species create a panel and add it to general form
+ for (PluginSpeciesAlias sp : this.species) {
+ JPanel panel = getPanelViewForSpecies(sp);
+ controlArea.add(panel);
+ }
+ // after adding all species add a text area which is "invisible", the main
+ // purpose of it is to fill the empty space in the form
+ JTextArea text = new JTextArea();
+ text.setEditable(false);
+ text.setBackground(frame.getBackground());
+ controlArea.add(text);
+
+ Container content = frame.getContentPane();
+ content.removeAll();
+
+ // the whole panel should be scrollable
+ JScrollPane scrollBar = new JScrollPane(controlArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
+ JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollBar.setPreferredSize(new Dimension(0, 0));
+ content.add(scrollBar);
+
+ frame.validate();
+ }
+
+ /**
+ * This method create a panel for a species with all information to be
+ * presented.
+ *
+ * @param species
+ * CellDesigner species alias
+ * @return {@link JPanel} object with information about species
+ */
+ private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
+ JPanel result = new JPanel();
+ result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
+
+ // create a caption
+ JPanel tmpPanel = new JPanel(new GridLayout(GRID_INFO_ROW_NUMBER, GRID_INFO_COL_NUMBER));
+ JLabel label = new JLabel("Element: ", JLabel.RIGHT);
+ label.setFont(captionFont);
+ tmpPanel.add(label, Component.RIGHT_ALIGNMENT);
+ JTextField textField = new JTextField(species.getSpecies().getName(), JLabel.LEFT);
+ textField.setFont(captionFont);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ tmpPanel.add(new JLabel("Alias id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
+ textField = new JTextField(species.getAliasID(), JLabel.LEFT);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ tmpPanel.add(new JLabel("Species id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
+ textField = new JTextField(species.getSpecies().getId(), JLabel.LEFT);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ result.add(tmpPanel);
+
+ // add empty space between labels
+ result.add(Box.createRigidArea(new Dimension(DISTANCE_BETWEEN_PANELS, DISTANCE_BETWEEN_PANELS)));
+
+ return result;
+ }
+
+ /**
+ * Returns info if the frame is visible.
+ *
+ * @return info if the frame is visible
+ */
+ public boolean isVisible() {
+ return frame.isVisible();
+ }
+
+ /**
+ * Sets frame title.
+ *
+ * @param title
+ * title of the frame
+ */
+ public void setTitle(String title) {
+ frame.setTitle(title);
+ }
+
+ /**
+ * Returns frame title.
+ *
+ * @return frame title
+ */
+ public JFrame getFrame() {
+ return frame;
+ }
+
+ /**
+ * Set {@link JFrame#defaultCloseOperation}.
+ *
+ * @param type
+ * new {@link JFrame#defaultCloseOperation} value
+ */
+ public void setDefaultCloseOperation(int type) {
+ frame.setDefaultCloseOperation(type);
+ }
+
+ /**
+ * Set {@link JFrame#setAlwaysOnTop(boolean)}.
+ *
+ * @param always
+ * new {@link JFrame#isAlwaysOnTop()} value
+ */
+ public void setAlwaysOnTop(boolean always) {
+ frame.setAlwaysOnTop(always);
+ }
}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
index dfe0ec3728a9195f03a8e44082d70fbc49ea854e..52c69f6440d96da4c8f73f9cafb954e693359ef1 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
@@ -9,13 +9,13 @@ import java.util.ArrayList;
import javax.swing.Timer;
+import org.apache.log4j.Logger;
+
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-import org.apache.log4j.Logger;
-
/**
* This class represent a plugin to CellDesigner that add info text box with
* informations about species. Plugin run in pooling mode (there is no other way
@@ -28,145 +28,146 @@ import org.apache.log4j.Logger;
*/
public class InfoPlugin extends CellDesignerPlugin {
- /**
- * What is the time between two consecutive checks if the set of selected
- * elements changed.
- */
- private static final int DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS = 250;
-
- /**
- * Maximum number of elements that will be described in the text box.
- */
- private static final int MAX_VISIBLE_ELEMENTS = 5;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(InfoPlugin.class.getName());
-
- /**
- * Listener called when set of selected elements in cell designer changed.
- */
- private ActionListener onChangeSelectListener;
-
- /**
- * Frame where visualization is generated.
- */
- private InfoFrame frame;
-
- /**
- * Default constructor. Creates menu and InfoFrame.
- */
- public InfoPlugin() {
- try {
- // load logger information
-
- // PropertyConfigurator.configure("D:/log4j.properties");
- logger.debug("Loading info plugin...");
-
- frame = InfoFrame.getInstance();
-
- // create keyboard listener for shortcuts
- KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
- public boolean dispatchKeyEvent(KeyEvent e) {
- if (KeyEvent.KEY_PRESSED == e.getID()) {
- // if someone hits CTRL+T then open/hide info window
- if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T && e.getModifiers() == java.awt.event.InputEvent.CTRL_MASK) {
- frame.setVisible(!frame.isVisible());
- return true;
- }
- }
- return false;
- }
- });
-
- // create a listener for refreshing selected elements
- onChangeSelectListener = new ActionListener() {
-
- /**
- * This string contains a simple hash of all species shown in the last
- * run of this listener. Due to this information we don't have to
- * refresh this information at every run.
- */
- private String selectedElementsId = "";
-
- @Override
- public void actionPerformed(ActionEvent arg0) {
-
- // if there is no open model then getSelectedAllNode() will throw an
- // exception...
- PluginListOf list = null;
- try {
- list = getSelectedAllNode();
- } catch (Exception e) {
- return;
- }
- try {
- ArrayList<PluginSpeciesAlias> v = new ArrayList<PluginSpeciesAlias>();
- String newId = "";
- // max five elements should be shown in infofrmae
- for (int i = 0; i < Math.min(list.size(), MAX_VISIBLE_ELEMENTS); i++) {
- if (list.get(i) instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) list.get(i);
- v.add(alias);
- newId += alias.getSpecies().getName();
- }
- }
- // if the cache is exactly the same as in the previous run then
- // don't update infoframe
- if (!selectedElementsId.equals(newId)) {
- selectedElementsId = newId;
- frame.setSpecies(v);
- }
- } catch (Exception exception) {
- logger.error(exception, exception);
- }
-
- }
- };
-
- Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
- timer.start();
-
- } catch (Exception exception) {
- logger.error("Unhandled exception. ", exception);
- }
- }
-
- // CHECKSTYLE:OFF
- @Override
- public void SBaseAdded(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseChanged(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
- // CHECKSTYLE:ON
-
- @Override
- public void addPluginMenu() {
- }
-
- @Override
- public void modelClosed(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelOpened(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelSelectChanged(PluginSBase arg0) {
-
- }
+ /**
+ * What is the time between two consecutive checks if the set of selected
+ * elements changed.
+ */
+ private static final int DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS = 250;
+
+ /**
+ * Maximum number of elements that will be described in the text box.
+ */
+ private static final int MAX_VISIBLE_ELEMENTS = 5;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(InfoPlugin.class.getName());
+
+ /**
+ * Listener called when set of selected elements in cell designer changed.
+ */
+ private ActionListener onChangeSelectListener;
+
+ /**
+ * Frame where visualization is generated.
+ */
+ private InfoFrame frame;
+
+ /**
+ * Default constructor. Creates menu and InfoFrame.
+ */
+ public InfoPlugin() {
+ try {
+ // load logger information
+
+ // PropertyConfigurator.configure("D:/log4j.properties");
+ logger.debug("Loading info plugin...");
+
+ frame = InfoFrame.getInstance();
+
+ // create keyboard listener for shortcuts
+ KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
+ public boolean dispatchKeyEvent(KeyEvent e) {
+ if (KeyEvent.KEY_PRESSED == e.getID()) {
+ // if someone hits CTRL+T then open/hide info window
+ if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T
+ && e.getModifiers() == java.awt.event.InputEvent.CTRL_MASK) {
+ frame.setVisible(!frame.isVisible());
+ return true;
+ }
+ }
+ return false;
+ }
+ });
+
+ // create a listener for refreshing selected elements
+ onChangeSelectListener = new ActionListener() {
+
+ /**
+ * This string contains a simple hash of all species shown in the last run of
+ * this listener. Due to this information we don't have to refresh this
+ * information at every run.
+ */
+ private String selectedElementsId = "";
+
+ @Override
+ public void actionPerformed(ActionEvent arg0) {
+
+ // if there is no open model then getSelectedAllNode() will throw an
+ // exception...
+ PluginListOf list = null;
+ try {
+ list = getSelectedAllNode();
+ } catch (Exception e) {
+ return;
+ }
+ try {
+ ArrayList<PluginSpeciesAlias> v = new ArrayList<PluginSpeciesAlias>();
+ String newId = "";
+ // max five elements should be shown in infofrmae
+ for (int i = 0; i < Math.min(list.size(), MAX_VISIBLE_ELEMENTS); i++) {
+ if (list.get(i) instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) list.get(i);
+ v.add(alias);
+ newId += alias.getSpecies().getName();
+ }
+ }
+ // if the cache is exactly the same as in the previous run then
+ // don't update infoframe
+ if (!selectedElementsId.equals(newId)) {
+ selectedElementsId = newId;
+ frame.setSpecies(v);
+ }
+ } catch (Exception exception) {
+ logger.error(exception, exception);
+ }
+
+ }
+ };
+
+ Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
+ timer.start();
+
+ } catch (Exception exception) {
+ logger.error("Unhandled exception. ", exception);
+ }
+ }
+
+ // CHECKSTYLE:OFF
+ @Override
+ public void SBaseAdded(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseChanged(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseDeleted(PluginSBase arg0) {
+ }
+
+ // CHECKSTYLE:ON
+
+ @Override
+ public void addPluginMenu() {
+ }
+
+ @Override
+ public void modelClosed(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelOpened(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelSelectChanged(PluginSBase arg0) {
+
+ }
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
index 311f2ff3bd00d6d38539f7c40937c92789cb75bf..cc230fa10816d3429385344e5d2bd98847a1b863 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
@@ -4,4 +4,3 @@
* {@link lcsb.mapviewer.cdplugin.info.InfoPlugin}.
*/
package lcsb.mapviewer.cdplugin.info;
-
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
index dc9a41e160029bf933b7e790b55660c481592e00..d1b7ccd956a2a69f1d8f6ab98a4ca55e0723e172 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
@@ -6,123 +6,125 @@ import static org.junit.Assert.assertNull;
import java.util.Set;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
public class CopyPasteAbstractActionTest {
- Logger logger = Logger.getLogger(CopyPasteAbstractActionTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPaste() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- String clipboardString = "[MIRIAM]\t" + MiriamRelationType.BQ_BIOL_IS.getStringRepresentation() + "\t" + MiriamType.CHEBI.getUris().get(0)
- + "\tCHEBI:12345\nasd";
- Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(clipboardString);
- assertNotNull(res);
- assertNotNull(res.getLeft());
- assertEquals(1, res.getLeft().size());
- assertNotNull(res.getRight());
- assertEquals("asd", res.getRight());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyPaste() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- String annString = "<rdf:RDF xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
- + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\" "
- + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"
- + "<rdf:Description rdf:about=\"#s1\">" + "<bqmodel:is>" + "<rdf:Bag>" + "<rdf:li rdf:resource=\"urn:miriam:hgnc:SNCA\"/>" + "</rdf:Bag>"
- + "</bqmodel:is>" + "</rdf:Description>" + "</rdf:RDF>";
-
- String str = pa.getCopyString(annString, "notes");
-
- Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(str);
- assertNotNull(res);
- assertNotNull(res.getLeft());
- assertEquals(1, res.getLeft().size());
- assertNotNull(res.getRight());
- assertEquals("notes", res.getRight());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerializeMiriam() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- MiriamData md = new MiriamData(MiriamType.CHEBI, "CH:12");
-
- String string = pa.serialize(md);
- MiriamData md2 = pa.deserialize(string);
- assertEquals(md, md2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize("ASDASDAS");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam2() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize(null);
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam3() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize("[MIRIAM]\tinvalid\ttype\tresource");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(CopyPasteAbstractActionTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPaste() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ String clipboardString = "[MIRIAM]\t" + MiriamRelationType.BQ_BIOL_IS.getStringRepresentation() + "\t"
+ + MiriamType.CHEBI.getUris().get(0)
+ + "\tCHEBI:12345\nasd";
+ Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(clipboardString);
+ assertNotNull(res);
+ assertNotNull(res.getLeft());
+ assertEquals(1, res.getLeft().size());
+ assertNotNull(res.getRight());
+ assertEquals("asd", res.getRight());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyPaste() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ String annString = "<rdf:RDF xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
+ + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\" "
+ + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"
+ + "<rdf:Description rdf:about=\"#s1\">" + "<bqmodel:is>" + "<rdf:Bag>"
+ + "<rdf:li rdf:resource=\"urn:miriam:hgnc:SNCA\"/>" + "</rdf:Bag>"
+ + "</bqmodel:is>" + "</rdf:Description>" + "</rdf:RDF>";
+
+ String str = pa.getCopyString(annString, "notes");
+
+ Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(str);
+ assertNotNull(res);
+ assertNotNull(res.getLeft());
+ assertEquals(1, res.getLeft().size());
+ assertNotNull(res.getRight());
+ assertEquals("notes", res.getRight());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerializeMiriam() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ MiriamData md = new MiriamData(MiriamType.CHEBI, "CH:12");
+
+ String string = pa.serialize(md);
+ MiriamData md2 = pa.deserialize(string);
+ assertEquals(md, md2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize("ASDASDAS");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam2() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize(null);
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam3() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize("[MIRIAM]\tinvalid\ttype\tresource");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}