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Relase 2.6.1
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Merge branch '2.6.1'
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@goglepox
goglepox committed Sep 30, 2013
2 parents b2c295f + 3417153 commit da4035c
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Showing 7 changed files with 98 additions and 51 deletions.
2 changes: 1 addition & 1 deletion net.bioclipse.metaprint2d.test/META-INF/MANIFEST.MF
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Expand Up @@ -2,7 +2,7 @@ Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: Metaprint2d test plugin
Bundle-SymbolicName: net.bioclipse.metaprint2d.test
Bundle-Version: 2.6.0.vqualifier
Bundle-Version: 2.6.1.qualifier
Bundle-Activator: net.bioclipse.metaprint2d.test.Activator
Bundle-Vendor: Ola Spjuth
Require-Bundle: org.eclipse.ui,
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2 changes: 1 addition & 1 deletion net.bioclipse.metaprint2d.ui/META-INF/MANIFEST.MF
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Expand Up @@ -2,7 +2,7 @@ Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: MetaPrint2D
Bundle-SymbolicName: net.bioclipse.metaprint2d.ui;singleton:=true
Bundle-Version: 2.6.0.vqualifier
Bundle-Version: 2.6.1.qualifier
Bundle-Activator: net.bioclipse.metaprint2d.ui.Activator
Bundle-Vendor: The Bioclipse Team
Eclipse-AutoStart: true
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71 changes: 46 additions & 25 deletions net.bioclipse.metaprint2d.ui/plugin.xml
View file
Expand Up @@ -126,24 +126,29 @@
<extension
point="org.eclipse.core.expressions.definitions">
<definition
id="net.bioclipse.definitions.activeMolEditor">
<with
variable="activeEditorId">
<or>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint">
</equals>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint.mdl">
</equals>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint.cml">
</equals>
<equals
value="net.bioclipse.cdk.ui.sdfeditor">
</equals>
</or>
</with>
id="net.bioclipse.definitions.showM2dUIElements">
<and>
<with
variable="activeEditorId">
<or>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint">
</equals>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint.mdl">
</equals>
<equals
value="net.bioclipse.cdk.ui.editors.jchempaint.cml">
</equals>
<equals
value="net.bioclipse.cdk.ui.sdfeditor">
</equals>
</or>
</with>
<with variable="activeWorkbenchWindow.activePerspective">
<equals value="net.bioclipse.metaprint2d.ui.Metaprint2dPerspective"/>
</with>
</and>
</definition>

</extension>
Expand All @@ -156,6 +161,12 @@
<menu
id="net.bioclipse.metaprint2d"
label="MetaPrint2D">
<visibleWhen
checkEnabled="false">
<with variable="activeWorkbenchWindow.activePerspective">
<equals value="net.bioclipse.metaprint2d.ui.Metaprint2dPerspective"/>
</with>
</visibleWhen>
</menu>
</menuContribution>

Expand Down Expand Up @@ -275,7 +286,7 @@
icon="icons/metaprint2d.gif"
tooltip="Execute MetaPrint2D on the active molecule(s)">
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>

Expand All @@ -286,7 +297,7 @@
icon="icons/molecule3D.gif"
tooltip="Set molecule coloring to CPK">
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>

Expand All @@ -298,7 +309,7 @@
tooltip="Turn on automatic MetaPrint2D calculation for the active molecule(s)"
style="toggle">
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>

Expand All @@ -314,7 +325,7 @@
value="All">
</parameter>
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>
<command
Expand All @@ -329,7 +340,7 @@
value="Dog">
</parameter>
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>
<command
Expand All @@ -344,7 +355,7 @@
value="Human">
</parameter>
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>
<command
Expand All @@ -359,14 +370,19 @@
value="Rat">
</parameter>
<visibleWhen>
<reference definitionId="net.bioclipse.definitions.activeMolEditor" />
<reference definitionId="net.bioclipse.definitions.showM2dUIElements" />
</visibleWhen>
</command>

<separator
name="additions"
visible="false">
</separator>
<!-- <visibleWhen>
<with variable="activeWorkbenchWindow.activePerspective">
<equals value="net.bioclipse.metaprint2d.ui.Metaprint2dPerspective"/>
</with>
</visibleWhen> -->
</toolbar>
</menuContribution>

Expand Down Expand Up @@ -442,12 +458,17 @@
</parameter>
<visibleWhen
checkEnabled="false">
<and>
<with
variable="activeEditor">
<instanceof
value="net.bioclipse.cdk.ui.sdfeditor.editor.MultiPageMoleculesEditorPart">
</instanceof>
</with>
<with variable="activeWorkbenchWindow.activePerspective">
<equals value="net.bioclipse.metaprint2d.ui.Metaprint2dPerspective"/>
</with>
</and>
</visibleWhen>
</command>
</menuContribution>
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2 changes: 1 addition & 1 deletion net.bioclipse.metaprint2d/META-INF/MANIFEST.MF
View file
Expand Up @@ -2,7 +2,7 @@ Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: Metaprint2d
Bundle-SymbolicName: net.bioclipse.metaprint2d;singleton:=true
Bundle-Version: 2.6.0.vqualifier
Bundle-Version: 2.6.1.qualifier
Bundle-Activator: net.bioclipse.metaprint2d.Activator
Require-Bundle: org.eclipse.ui,
org.eclipse.core.runtime
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43 changes: 21 additions & 22 deletions net.bioclipse.metaprint2d/src/net/bioclipse/metaprint2d/Metaprinter.java
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Expand Up @@ -10,7 +10,6 @@
******************************************************************************/
package net.bioclipse.metaprint2d;

import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
Expand Down Expand Up @@ -41,12 +40,12 @@ public class Metaprinter {

private static final Logger logger = Logger.getLogger(Metaprinter.class);

public static final Color RED_COLOR=new Color(200,70,70);
public static final Color GREEN_COLOR=new Color(00,200,80);
public static final Color AMBER_COLOR=new Color(255,191,0);

public static final Color BLACK_COLOR = new Color(150,150,150);
public static final Color WHITE_COLOR = new Color(255,255,255);
// public static final Color RED_COLOR=new Color(200,70,70);
// public static final Color GREEN_COLOR=new Color(00,200,80);
// public static final Color AMBER_COLOR=new Color(255,191,0);
//
// public static final Color BLACK_COLOR = new Color(150,150,150);
// public static final Color WHITE_COLOR = new Color(255,255,255);

// private static final String DATAFILE_ALL = "/data/metab2008.1-all.bin";
// private static final String DATAFILE_DOG = "/data/metab2008.1-dog.bin";
Expand Down Expand Up @@ -222,21 +221,21 @@ private static File getDataFile(Species species) {


//This is the metaprint cutoff
public static Color getColorByMetprint( MetaPrintResult res ) {

double ratio=res.getNormalisedRatio();

if (ratio>0.66){
return Metaprinter.RED_COLOR;
}
else if (0.66>=ratio && ratio>0.33){
return Metaprinter.AMBER_COLOR;
}
else if (0.33>=ratio && ratio>0.15){
return Metaprinter.GREEN_COLOR;
}
return null;
}
// public static Color getColorByMetprint( MetaPrintResult res ) {
//
// double ratio=res.getNormalisedRatio();
//
// if (ratio>0.66){
// return Metaprinter.RED_COLOR;
// }
// else if (0.66>=ratio && ratio>0.33){
// return Metaprinter.AMBER_COLOR;
// }
// else if (0.33>=ratio && ratio>0.15){
// return Metaprinter.GREEN_COLOR;
// }
// return null;
// }

public static void setSpecies( String parm ) {

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2 changes: 1 addition & 1 deletion net.bioclipse.metaprint2d_feature/feature.xml
View file
Expand Up @@ -2,7 +2,7 @@
<feature
id="net.bioclipse.metaprint2d_feature"
label="MetaPrint2D"
version="2.6.0.vqualifier"
version="2.6.1.qualifier"
provider-name="bioclipse.net"
plugin="net.bioclipse.metaprint2d.ui">

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27 changes: 27 additions & 0 deletions net.bioclipse.metaprint2d_releng/buckminster.cspec
View file
@@ -0,0 +1,27 @@
<?xml version="1.0" encoding="UTF-8"?>
<cspec xmlns="http://www.eclipse.org/buckminster/CSpec-1.0" name="net.bioclipse.metaprint2d_releng" componentType="buckminster" version="2.6.1">
<dependencies>
<dependency name="net.bioclipse.metaprint2d_feature" componentType="eclipse.feature" />
<dependency name="org.slf4j.api" componentType="osgi.bundle"/>
<dependency name="log4j.over.slf4j" componentType="osgi.bundle"/>
<dependency name="org.eclipse.rcp" componentType="eclipse.feature"/>
<!--
<dependency name="slf4j.api" componentType="osgi.bundle"/>
<dependency name="jcl.over.slf4j" componentType="osgi.bundle"/>
<dependency name="log4j.over.slf4j" componentType="osgi.bundle"/>
-->
</dependencies>
<actions>
<public name="site.mirror.p2" actor="p2SiteMirror">
<prerequisites>
<attribute name="site.p2" alias="site"/>
</prerequisites>
<products base="${bioclipse.mirror}/${bioclipse.mirror.name}" upToDatePolicy="ACTOR" />
</public>
</actions>
<groups>
<public name="site.p2">
<attribute name="site.p2" component="net.bioclipse.metaprint2d_feature"/>
</public>
</groups>
</cspec>

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