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JAL-845 preparation for awareness of AlignFrame in SplitFrame for save
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 3 Feb 2015 16:49:47 +0000
(16:49 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 3 Feb 2015 16:49:47 +0000
(16:49 +0000)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
d3a7e2c
..
f08306a
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-336,7
+336,7
@@
public class Jalview2XML
*/
public void SaveState(JarOutputStream jout)
{
*/
public void SaveState(JarOutputStream jout)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames(); // Desktop.desktop.getAllFrames();
if (frames == null)
{
if (frames == null)
{
@@
-353,71
+353,66
@@
public class Jalview2XML
// NOTE ALSO new PrintWriter must be used for each new JarEntry
PrintWriter out = null;
// NOTE ALSO new PrintWriter must be used for each new JarEntry
PrintWriter out = null;
- Vector shortNames = new Vector();
+ List<String> shortNames = new ArrayList<String>();
// REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
// REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
- if (frames[i] instanceof AlignFrame)
+ AlignFrame af = frames[i];
+ // skip ?
+ if (skipList != null
+ && skipList
+ .containsKey(af.getViewport().getSequenceSetId()))
{
{
- AlignFrame af = (AlignFrame) frames[i];
- // skip ?
- if (skipList != null
- && skipList.containsKey(af.getViewport()
- .getSequenceSetId()))
- {
- continue;
- }
+ continue;
+ }
- String shortName = af.getTitle();
+ String shortName = af.getTitle();
- if (shortName.indexOf(File.separatorChar) > -1)
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
{
{
- shortName = shortName.substring(shortName
- .lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
}
}
- int count = 1;
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
- while (shortNames.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName
- .substring(0, shortName.lastIndexOf("_"));
- }
+ shortNames.add(shortName);
- shortName = shortName.concat("_" + count);
- count++;
- }
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
- shortNames.addElement(shortName);
+ int apSize = af.alignPanels.size();
- if (!shortName.endsWith(".xml"))
+ for (int ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = af.alignPanels.get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
{
{
- shortName = shortName + ".xml";
+ fileName = fileName + ".xml";
}
}
- int ap, apSize = af.alignPanels.size();
+ SaveState(apanel, fileName, jout);
- for (ap = 0; ap < apSize; ap++)
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
{
{
- AlignmentPanel apanel = af.alignPanels.get(ap);
- String fileName = apSize == 1 ? shortName : ap + shortName;
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
- SaveState(apanel, fileName, jout);
-
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
-
+ dsses.put(dssid, af);
}
}
}
}
}
}