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JAL-3451 JalviewJS embedded mode not resizing
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
2efa0fb
..
3d80589
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-305,6
+305,15
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
+
+ if (aparser.contains(ArgsParser.NODISPLAY)
+ || aparser.contains(ArgsParser.NOGUI)
+ || aparser.contains(ArgsParser.HEADLESS)
+ || "true".equals(System.getProperty("java.awt.headless")))
+ {
+ headless = true;
+ }
+
if (isJS)
{
isJavaAppletTag = aparser.isApplet();
if (isJS)
{
isJavaAppletTag = aparser.isApplet();
@@
-336,13
+345,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
showUsage();
System.exit(0);
}
showUsage();
System.exit(0);
}
- if (aparser.contains(ArgsParser.NODISPLAY)
- || aparser.contains(ArgsParser.NOGUI)
- || aparser.contains(ArgsParser.HEADLESS)
- || "true".equals(System.getProperty("java.awt.headless")))
- {
- headless = true;
- }
+
// anything else!
// anything else!
@@
-398,7
+401,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
try
{
try
{
- if (Platform.isWin())
+ if (!isJS && Platform.isWin())
{
UIManager.setLookAndFeel(
headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
{
UIManager.setLookAndFeel(
headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
@@
-855,11
+858,11
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
+ "] executed successfully!");
groovyscript = null;
}
+ "] executed successfully!");
groovyscript = null;
}
- checkOutputFile(aparser, af, format);
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
- }
+ }
+ checkOutputFile(aparser, af, format);
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
}
}
}
@@
-1049,6
+1052,8
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
// biojsmsa filename
String outputFormat = aparser.nextValue();
String file = aparser.nextValue();
// biojsmsa filename
String outputFormat = aparser.nextValue();
String file = aparser.nextValue();
+ System.out.println("format " + outputFormat);
+
if (outputFormat.equalsIgnoreCase("png"))
{
af.createPNG(new File(file));
if (outputFormat.equalsIgnoreCase("png"))
{
af.createPNG(new File(file));
@@
-1638,6
+1643,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public String getSelectedSequencesFrom(AlignFrameI alf)
{
@Override
public String getSelectedSequencesFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return getSelectedSequencesFrom(alf, null);
}
return getSelectedSequencesFrom(alf, null);
}
@@
-1649,6
+1658,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
@Override
public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesFrom(alf, sep);
}
return appLoader.getSelectedSequencesFrom(alf, sep);
}
@@
-1661,7
+1674,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public void highlight(String sequenceId, String position,
String alignedPosition)
{
public void highlight(String sequenceId, String position,
String alignedPosition)
{
- highlightIn(getCurrentAlignFrame(), sequenceId, position,
+ highlightIn(null, sequenceId, position,
alignedPosition);
}
alignedPosition);
}
@@
-1669,6
+1682,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition)
{
public void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
}
appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
}
@@
-1681,7
+1698,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public void select(String sequenceIds, String columns, String sep)
{
@Override
public void select(String sequenceIds, String columns, String sep)
{
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
+ selectIn(null, sequenceIds, columns, sep);
}
@Override
}
@Override
@@
-1694,6
+1711,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
String sep)
{
public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.selectIn(alf, sequenceIds, columns, sep);
}
appLoader.selectIn(alf, sequenceIds, columns, sep);
}
@@
-1701,7
+1722,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
format, suffix);
}
@@
-1709,6
+1730,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String sep)
{
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
@@
-1727,6
+1752,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
@Override
public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAlignmentOrderFrom(alf, sep);
}
return appLoader.getAlignmentOrderFrom(alf, sep);
}
@@
-1746,6
+1775,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
@@
-1783,6
+1816,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
@Override
public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.loadAnnotationFrom(alf, annotation);
}
appLoader.loadAnnotationFrom(alf, annotation);
}
@@
-1796,43
+1833,55
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
- return getFeaturesFrom(getCurrentAlignFrame(), format);
+ return getFeaturesFrom(null, format);
}
@Override
public String getFeaturesFrom(AlignFrameI alf, String format)
{
}
@Override
public String getFeaturesFrom(AlignFrameI alf, String format)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeaturesFrom(alf, format);
}
@Override
public String getAnnotation()
{
return appLoader.getFeaturesFrom(alf, format);
}
@Override
public String getAnnotation()
{
- return getAnnotationFrom(getCurrentAlignFrame());
+ return getAnnotationFrom(null);
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
- return newViewFrom(getCurrentAlignFrame(), null);
+ return newViewFrom(null, null);
}
@Override
public AlignFrameI newView(String name)
{
}
@Override
public AlignFrameI newView(String name)
{
- return newViewFrom(getCurrentAlignFrame(), name);
+ return newViewFrom(null, name);
}
@Override
}
@Override
@@
-1844,6
+1893,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public AlignFrameI newViewFrom(AlignFrameI alf, String name)
{
@Override
public AlignFrameI newViewFrom(AlignFrameI alf, String name)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.newViewFrom(alf, name);
}
return appLoader.newViewFrom(alf, name);
}
@@
-1858,6
+1911,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
pdbFile);
}
return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
pdbFile);
}
@@
-1866,56
+1923,80
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn)
{
public void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToColumnIn(alf, leftHandColumn);
}
@Override
public String getFeatureGroups()
{
appLoader.scrollViewToColumnIn(alf, leftHandColumn);
}
@Override
public String getFeatureGroups()
{
- return getFeatureGroupsOn(getCurrentAlignFrame());
+ return getFeatureGroupsOn(null);
}
@Override
public String getFeatureGroupsOn(AlignFrameI alf)
{
}
@Override
public String getFeatureGroupsOn(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOn(alf);
}
@Override
public String getFeatureGroupsOfState(boolean visible)
{
return appLoader.getFeatureGroupsOn(alf);
}
@Override
public String getFeatureGroupsOfState(boolean visible)
{
- return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+ return getFeatureGroupsOfStateOn(null, visible);
}
@Override
public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
}
@Override
public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOfStateOn(alf, visible);
}
@Override
return appLoader.getFeatureGroupsOfStateOn(alf, visible);
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
- boolean state)
- {
- setFeatureGroupStateOn(alf, groups, state);
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
}
@Override
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
{
{
- appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
}
@Override
}
@Override
@@
-1950,7
+2031,11
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public Object openTreePanel(AlignFrame af, String treeType,
String modelName)
@Override
public Object openTreePanel(AlignFrame af, String treeType,
String modelName)
- {
+ { // JalviewJS api
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
@@
-1966,6
+2051,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
@Override
public Object openPcaPanel(AlignFrame af, String modelName)
{
@Override
public Object openPcaPanel(AlignFrame af, String modelName)
{
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openPcaPanel(af, modelName, null);
}
return CalculationChooser.openPcaPanel(af, modelName, null);
}
@@
-1973,7
+2062,7
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public String getSelectedSequencesAsAlignment(String format,
boolean suffix)
{
public String getSelectedSequencesAsAlignment(String format,
boolean suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
format, suffix);
}
@@
-1981,6
+2070,10
@@
public class Jalview implements ApplicationSingletonI, JalviewJSApi
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, boolean suffix)
{
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, boolean suffix)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
"" + suffix);
}
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
"" + suffix);
}