From ee9b37d729a18473bace12991256a8c7dea97c5e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 9 Jul 2018 09:05:13 +0200
Subject: [PATCH] antisense rna region has width with absolute values instead
of CellDesigner relative values
---
.../species/AntisenseRnaXmlParser.java | 4 +-
.../CellDesignerAntisenseRnaRegion.java | 2 +-
.../map/species/field/AntisenseRnaRegion.java | 58 ++++++-------------
.../species/AntisenseRnaComparatorTest.java | 2 +-
.../species/field/AntisenseRnaRegionTest.java | 14 +----
.../src/db/12.1.0~alpha.0/fix_db_20180709.sql | 8 +++
.../dao/map/layout/alias/AliasDaoTest2.java | 4 +-
7 files changed, 35 insertions(+), 57 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index ee2c84aa36..bacf3f3ae2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -125,8 +125,8 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
if (!region.getName().equals("")) {
attributes += " name=\"" + escapeXml(region.getName()) + "\"";
}
- if (region.getSize() != 0) {
- attributes += " size=\"" + region.getSize() + "\"";
+ if (region.getWidth() != 0) {
+ attributes += " size=\"" + region.getWidth() / region.getSpecies().getWidth() + "\"";
}
if (region.getPosition() != null) {
double pos = (region.getPosition().getX() - region.getSpecies().getWidth())
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
index ec607f2dfe..09c29bb954 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
@@ -329,7 +329,7 @@ public class CellDesignerAntisenseRnaRegion implements Serializable {
AntisenseRnaRegion result = new AntisenseRnaRegion();
result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
result.setName(name);
- result.setSize(size);
+ result.setWidth(element.getWidth()*size);
result.setPosition(new Point2D.Double(element.getX() + element.getWidth() * 3.0 / 4.0 * pos, element.getY()));
result.setType(type);
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 2691644b16..c75979518d 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
@@ -44,7 +44,7 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
/**
* Default size of the object (in graphical representation).
*/
- private static final double DEFAULT_SIZE = 0.1;
+ private static final double DEFAULT_SIZE = 10;
/**
* Default class logger.
@@ -85,10 +85,10 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
private AntisenseRnaRegionType type;
/**
- * Size of the region in the graphic representation.
+ * Width of the region in the graphic representation.
*/
- @Column(name = "size")
- private double size = DEFAULT_SIZE;
+ @Column(name = "width")
+ private double width = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
@@ -121,9 +121,11 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
public AntisenseRnaRegion(AntisenseRnaRegion original) {
this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
this.name = original.name;
- this.size = original.size;
this.type = original.type;
- this.setPosition(original.getPosition());
+ Point2D position = new Point2D.Double();
+ position.setLocation(original.getPosition());
+ this.setPosition(position);
+ this.setWidth(original.getWidth());
}
/**
@@ -140,21 +142,6 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
}
- /**
- * Sets size from the string.
- *
- * @param text
- * size to parse and set
- * @see #size
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
- }
-
/**
* Update data in this object from parameter (only if values in parameter object
* are valid).
@@ -167,7 +154,7 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
&& !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
throw new InvalidArgumentException("Cannot update from mr with different id");
}
- this.size = mr.getSize();
+ this.setWidth(mr.getWidth());
if (mr.getName() != null) {
this.name = mr.getName();
}
@@ -180,7 +167,7 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
@Override
public String toString() {
String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPosition() + ","
- + getSize() + ",";
+ + getWidth() + ",";
return result;
}
@@ -243,23 +230,6 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
this.type = type;
}
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(double size) {
- this.size = size;
- }
-
/**
* @return the species
* @see #species
@@ -301,4 +271,12 @@ public class AntisenseRnaRegion implements Serializable, ElementModification {
public void setPosition(Point2D position) {
this.position = position;
}
+
+ public double getWidth() {
+ return width;
+ }
+
+ public void setWidth(double width) {
+ this.width = width;
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index 3f8a0ab148..8ee9493bb1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -84,7 +84,7 @@ public class AntisenseRnaComparatorTest {
region1.setIdAntisenseRnaRegion("a");
region1.setName("name");
region1.setPosition(new Point2D.Double(0, 1));
- region1.setSize("2");
+ region1.setWidth(2);
region1.setType(AntisenseRnaRegionType.CODING_REGION);
return result;
}
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 cb1e7efa20..7bc3646490 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
@@ -89,7 +89,7 @@ public class AntisenseRnaRegionTest {
int id = 91;
AntisenseRna species = new AntisenseRna("id");
Point2D position = new Point2D.Double(10, 20);
- double size = 5.3;
+ double width = 5.3;
AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
String name = "nam";
String idAntisenseRnaRegion = "iddd";
@@ -97,7 +97,7 @@ public class AntisenseRnaRegionTest {
region.setId(id);
region.setSpecies(species);
region.setPosition(position);
- region.setSize(size);
+ region.setWidth(width);
region.setType(type);
region.setName(name);
region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
@@ -105,19 +105,11 @@ public class AntisenseRnaRegionTest {
assertEquals(id, region.getId());
assertEquals(species, region.getSpecies());
assertEquals(position.distance(region.getPosition()), 0, Configuration.EPSILON);
- assertEquals(size, region.getSize(), Configuration.EPSILON);
+ assertEquals(width, region.getWidth(), Configuration.EPSILON);
assertEquals(type, region.getType());
assertEquals(name, region.getName());
assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
- try {
- region.setSize("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- region.setSize("1.0");
- assertEquals(1.0, region.getSize(), Configuration.EPSILON);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql
index ec463fbdab..5c5283269f 100644
--- a/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql
@@ -6,3 +6,11 @@ update antisense_rna_region_table set type_string ='CODING_REGION' where type =1
update antisense_rna_region_table set type_string ='PROTEIN_BINDING_DOMAIN' where type =2;
alter table antisense_rna_region_table drop column type;
alter table antisense_rna_region_table rename COLUMN type_string to type;
+
+-- antisense region doesn't have state
+alter table antisense_rna_region_table drop column state;
+
+--size is changed to width for antisense rna region
+alter table antisense_rna_region_table add column width numeric(6,2);
+update antisense_rna_region_table set width=element_table.width*antisense_rna_region_table.size from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and not size is null;
+alter table antisense_rna_region_table drop column size;
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 c1831f210e..58d106086b 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
@@ -181,7 +181,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
AntisenseRna sp = new AntisenseRna(testIdAlias);
AntisenseRnaRegion mr = new AntisenseRnaRegion();
mr.setName("name");
- mr.setSize(3.0);
+ mr.setWidth(3.0);
mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
sp.addRegion(mr);
@@ -197,7 +197,7 @@ 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).getWidth(), mr.getWidth(), EPSILON);
assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
aliasDao.delete(sp2);
--
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