From 3ef46380b5e6d0b3262f753e1e6b07a469df2378 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 6 Jul 2018 15:12:48 +0200
Subject: [PATCH] antisense rna are visualized
---
.../species/AntisenseRnaConverter.java | 20 ++---------------
.../map/species/field/AntisenseRnaRegion.java | 22 +------------------
.../species/field/AntisenseRnaRegionTest.java | 6 +----
.../dao/map/layout/alias/AliasDaoTest2.java | 2 --
.../elements/ElementRestImplTest.java | 1 -
5 files changed, 4 insertions(+), 47 deletions(-)
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index f2ee56366f..5698bc78d5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -60,7 +60,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
graphics.setStroke(stroke);
for (AntisenseRnaRegion mr : antisenseRna.getRegions()) {
- drawRegion(antisenseRna, mr, graphics, false, false);
+ drawRegion(antisenseRna, mr, graphics, false);
}
drawText(antisenseRna, graphics, params);
@@ -99,16 +99,11 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
* {@link AntisenseRnaRegion} to be drawn
* @param graphics
* {@link Graphics2D} where we draw region
- * @param drawEmptyRegion
- * flag determining if we should draw empty regions
* @param drawDescription
* flag determining if we want to draw description as well
*/
private void drawRegion(final AntisenseRna antisenseRna, final AntisenseRnaRegion region, final Graphics2D graphics,
- final boolean drawEmptyRegion, final boolean drawDescription) {
- if ((!drawEmptyRegion) && (region.getState() == null)) {
- return;
- }
+ final boolean drawDescription) {
double diameter = DEFAULT_MODIFICATION_DIAMETER;
double y = antisenseRna.getY();
@@ -129,16 +124,5 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
}
- ModificationState state = region.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) textX, (int) textY);
- graphics.setFont(tmpFont);
- }
-
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
index 3afc4835f9..ab856497bc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
@@ -70,14 +70,6 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
@Column(name = "name")
private String name = "";
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- @Column(name = "state")
- private ModificationState state = null;
-
/**
* Type of the region in the rna. There are three possible values:
* <ul>
@@ -173,9 +165,6 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
throw new InvalidArgumentException("Cannot update from mr with different id");
}
this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
if (mr.getName() != null) {
this.name = mr.getName();
}
@@ -231,16 +220,7 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
* @see #state
*/
public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
+ return null;
}
/**
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
index 9f91ffb5ad..cb1e7efa20 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
@@ -55,12 +55,11 @@ public class AntisenseRnaRegionTest {
public void testUpdate() {
try {
AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- antisenseRna.setState(ModificationState.EMPTY);
antisenseRna.setName("as");
antisenseRna.setPosition(new Point2D.Double(10, 0));
AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
antisenseRna2.update(antisenseRna);
- assertEquals(antisenseRna.getState(), antisenseRna2.getState());
+ assertEquals(antisenseRna.getName(), antisenseRna2.getName());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -102,7 +101,6 @@ public class AntisenseRnaRegionTest {
region.setType(type);
region.setName(name);
region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- region.setState(ModificationState.ACETYLATED);
assertEquals(id, region.getId());
assertEquals(species, region.getSpecies());
@@ -112,8 +110,6 @@ public class AntisenseRnaRegionTest {
assertEquals(name, region.getName());
assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
- assertEquals(ModificationState.ACETYLATED, region.getState());
-
try {
region.setSize("text");
fail("Exception expected");
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index 1aefeefe03..c1831f210e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -183,7 +183,6 @@ public class AliasDaoTest2 extends PersistTestFunctions {
mr.setName("name");
mr.setSize(3.0);
mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
- mr.setState(ModificationState.UNKNOWN);
sp.addRegion(mr);
aliasDao.add(sp);
@@ -199,7 +198,6 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(sp2.getRegions().get(0).getIdAntisenseRnaRegion(), mr.getIdAntisenseRnaRegion());
assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
- assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
aliasDao.delete(sp2);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index a5a06edbce..9acc7706aa 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -160,7 +160,6 @@ public class ElementRestImplTest extends RestTestFunctions {
String state = "asd";
AntisenseRna antisenseRna = new AntisenseRna("s1");
AntisenseRnaRegion mr = new AntisenseRnaRegion();
- mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
antisenseRna.addRegion(mr);
antisenseRna.setState(state);
--
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