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Loads PDB files from jar file, new views can open PDB file
author
amwaterhouse
<Andrew Waterhouse>
Tue, 28 Nov 2006 10:19:53 +0000
(10:19 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 28 Nov 2006 10:19:53 +0000
(10:19 +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
e6191de
..
8a4c669
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-335,19
+335,20
@@
public class Jalview2XML
pdb.setId(entry.getId());
pdb.setType(entry.getType());
pdb.setId(entry.getId());
pdb.setType(entry.getType());
+
if(entry.getFile()!=null)
{
if(entry.getFile()!=null)
{
+ pdb.setFile(entry.getFile());
if(pdbfiles==null)
pdbfiles = new Vector();
if(pdbfiles==null)
pdbfiles = new Vector();
-
if(!pdbfiles.contains(entry.getId()))
{
pdbfiles.addElement(entry.getId());
try
{
File file = new File(entry.getFile());
if(!pdbfiles.contains(entry.getId()))
{
pdbfiles.addElement(entry.getId());
try
{
File file = new File(entry.getFile());
- if(file.exists())
+ if(file.exists() && jout!=null)
{
byte[] data = new byte[ (int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
{
byte[] data = new byte[ (int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
@@
-981,6
+982,7
@@
public class Jalview2XML
String loadPDBFile(String file, String pdbId)
{
String loadPDBFile(String file, String pdbId)
{
+ System.out.println(file +" "+pdbId);
try
{
JarInputStream jin = null;
try
{
JarInputStream jin = null;
@@
-1003,6
+1005,7
@@
public class Jalview2XML
BufferedReader in = new BufferedReader(new InputStreamReader(jin));
File outFile = File.createTempFile("jalview_pdb", ".txt");
BufferedReader in = new BufferedReader(new InputStreamReader(jin));
File outFile = File.createTempFile("jalview_pdb", ".txt");
+ System.out.println("CREATE "+outFile);
outFile.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
outFile.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
@@
-1410,8
+1413,7
@@
public class Jalview2XML
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
@@
-1437,6
+1439,8
@@
public class Jalview2XML
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
ColourSchemeI cs = null;
ColourSchemeI cs = null;