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Stockholm parser added
author
amwaterhouse
<Andrew Waterhouse>
Mon, 14 Aug 2006 16:10:00 +0000
(16:10 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Mon, 14 Aug 2006 16:10:00 +0000
(16:10 +0000)
src/jalview/appletgui/APopupMenu.java
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src/jalview/appletgui/AlignFrame.java
patch
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src/jalview/gui/PopupMenu.java
patch
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src/jalview/io/AppletFormatAdapter.java
patch
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src/jalview/io/IdentifyFile.java
patch
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src/jalview/jbgui/GAlignFrame.java
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diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
be4a599
..
b26bd74
100755
(executable)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-89,7
+89,7
@@
public class APopupMenu
e.printStackTrace();
\r
}
\r
\r
e.printStackTrace();
\r
}
\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
\r
{
\r
MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
elementAt(
\r
{
\r
MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
elementAt(
\r
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
9ba6cca
..
1ff729d
100755
(executable)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-1937,7
+1937,7
@@
public void itemStateChanged(ItemEvent evt)
MenuItem item;
\r
\r
// dynamically fill save as menu with available formats
\r
MenuItem item;
\r
\r
// dynamically fill save as menu with available formats
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
\r
{
\r
\r
item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
{
\r
\r
item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
35ca39b
..
9764f4a
100755
(executable)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-115,7
+115,7
@@
public class PopupMenu extends JPopupMenu
colours.add(PIDColour);
\r
colours.add(BLOSUM62Colour);
\r
\r
colours.add(PIDColour);
\r
colours.add(BLOSUM62Colour);
\r
\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
\r
{
\r
JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
elementAt(
\r
{
\r
JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
elementAt(
\r
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
8d2d796
..
ba5b8a0
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-48,6
+48,7
@@
formats.addElement("PileUp");
\r
formats.addElement("PIR");
\r
formats.addElement("PFAM");
\r
formats.addElement("PileUp");
\r
formats.addElement("PIR");
\r
formats.addElement("PFAM");
\r
+ formats.addElement("STH");
\r
formats.addElement("PDB");
\r
}
\r
\r
formats.addElement("PDB");
\r
}
\r
\r
@@
-57,6
+58,7
@@
public static String PASTE = "Paste";
\r
public static String CLASSLOADER = "ClassLoader";
\r
\r
public static String PASTE = "Paste";
\r
public static String CLASSLOADER = "ClassLoader";
\r
\r
+
\r
AlignFile afile = null;
\r
String inFile;
\r
\r
AlignFile afile = null;
\r
String inFile;
\r
\r
@@
-112,6
+114,11
@@
{
\r
afile = new MCview.PDBfile(inFile, type);
\r
}
\r
{
\r
afile = new MCview.PDBfile(inFile, type);
\r
}
\r
+ else if (format.equals("STH"))
\r
+ {
\r
+ afile = new StockholmFile(inFile, type);
\r
+ }
\r
+
\r
\r
return afile.getSeqsAsArray();
\r
}
\r
\r
return afile.getSeqsAsArray();
\r
}
\r
@@
-196,6
+203,11
@@
{
\r
afile = new PfamFile();
\r
}
\r
{
\r
afile = new PfamFile();
\r
}
\r
+ else if (format.equalsIgnoreCase("STH"))
\r
+ {
\r
+ afile = new StockholmFile();
\r
+ }
\r
+
\r
\r
afile.addJVSuffix(jvsuffix);
\r
\r
\r
afile.addJVSuffix(jvsuffix);
\r
\r
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
348b085
..
5d39383
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-76,6
+76,13
@@
public class IdentifyFile
{
\r
data = data.toUpperCase();
\r
\r
{
\r
data = data.toUpperCase();
\r
\r
+ if ( (data.indexOf("# STOCKHOLM") > -1))
\r
+ {
\r
+ reply = "STH";
\r
+
\r
+ break;
\r
+ }
\r
+
\r
if ((data.indexOf("#") == 0) || (data.length() < 1))
\r
{
\r
continue;
\r
if ((data.indexOf("#") == 0) || (data.length() < 1))
\r
{
\r
continue;
\r
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
b7c903e
..
496585b
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-148,7
+148,7
@@
public class GAlignFrame
setJMenuBar(alignFrameMenuBar);
\r
\r
// dynamically fill save as menu with available formats
\r
setJMenuBar(alignFrameMenuBar);
\r
\r
// dynamically fill save as menu with available formats
\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
\r
{
\r
JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
elementAt(
\r
{
\r
JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
elementAt(
\r