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WRITEABLE_FORMATS and READABLE_FORMATS string []
author
amwaterhouse
<Andrew Waterhouse>
Tue, 15 Aug 2006 10:02:12 +0000
(10:02 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 15 Aug 2006 10:02:12 +0000
(10:02 +0000)
src/jalview/appletgui/APopupMenu.java
patch
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blob
|
history
src/jalview/appletgui/AlignFrame.java
patch
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src/jalview/bin/JalviewLite.java
patch
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src/jalview/gui/CutAndPasteTransfer.java
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src/jalview/gui/PopupMenu.java
patch
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src/jalview/gui/SequenceFetcher.java
patch
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history
src/jalview/io/AppletFormatAdapter.java
patch
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history
src/jalview/io/FileLoader.java
patch
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history
src/jalview/jbgui/GAlignFrame.java
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history
src/jalview/ws/JPredClient.java
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blob
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history
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
b26bd74
..
449b83a
100755
(executable)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-89,11
+89,10
@@
public class APopupMenu
e.printStackTrace();
\r
}
\r
\r
e.printStackTrace();
\r
}
\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
{
\r
{
\r
- MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
- elementAt(
\r
- i));
\r
+ MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
\r
+
\r
item.addActionListener(this);
\r
outputmenu.add(item);
\r
}
\r
item.addActionListener(this);
\r
outputmenu.add(item);
\r
}
\r
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
1ff729d
..
eb6fe49
100755
(executable)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-1937,12
+1937,11
@@
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()-2; i++)
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
{
\r
\r
{
\r
\r
- item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
- elementAt(
\r
- i));
\r
+ item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
+
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
53d55f3
..
10efeeb
100755
(executable)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-337,6
+337,7
@@
public class JalviewLite extends Applet
param = getParameter("showFeatureSettings");
\r
if(param !=null && param.equalsIgnoreCase("true"))
\r
{
\r
param = getParameter("showFeatureSettings");
\r
if(param !=null && param.equalsIgnoreCase("true"))
\r
{
\r
+ currentAlignFrame.viewport.showSequenceFeatures(true);
\r
currentAlignFrame.featureSettings_actionPerformed();
\r
}
\r
\r
currentAlignFrame.featureSettings_actionPerformed();
\r
}
\r
\r
diff --git
a/src/jalview/gui/CutAndPasteTransfer.java
b/src/jalview/gui/CutAndPasteTransfer.java
index
2bb456b
..
5c9c941
100755
(executable)
--- a/
src/jalview/gui/CutAndPasteTransfer.java
+++ b/
src/jalview/gui/CutAndPasteTransfer.java
@@
-169,7
+169,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
String format = new IdentifyFile().Identify(getText(), "Paste");
\r
SequenceI[] sequences = null;
\r
\r
String format = new IdentifyFile().Identify(getText(), "Paste");
\r
SequenceI[] sequences = null;
\r
\r
- if (FormatAdapter.formats.contains(format))
\r
+ if (FormatAdapter.isValidFormat(format))
\r
{
\r
try{
\r
sequences = new FormatAdapter().readFile(getText(), "Paste", format);
\r
{
\r
try{
\r
sequences = new FormatAdapter().readFile(getText(), "Paste", format);
\r
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
9764f4a
..
e89eb28
100755
(executable)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-115,11
+115,10
@@
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()-2; i++)
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
{
\r
{
\r
- JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
- elementAt(
\r
- i));
\r
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
\r
+
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
99c1d5e
..
f3d8e29
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-364,7
+364,7
@@
public class SequenceFetcher
String format = new IdentifyFile().Identify(result, "Paste");
\r
SequenceI[] sequences = null;
\r
\r
String format = new IdentifyFile().Identify(result, "Paste");
\r
SequenceI[] sequences = null;
\r
\r
- if (FormatAdapter.formats.contains(format))
\r
+ if (FormatAdapter.isValidFormat(format))
\r
{
\r
sequences = null;
\r
try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
\r
{
\r
sequences = null;
\r
try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
\r
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
ba5b8a0
..
1de01e6
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-32,26
+32,22
@@
public class AppletFormatAdapter
\r
{
\r
/** DOCUMENT ME!! */
\r
public class AppletFormatAdapter
\r
{
\r
/** DOCUMENT ME!! */
\r
- public static final Vector formats = new Vector();
\r
+ public static final String [] READABLE_FORMATS = new String[]
\r
+ {
\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
\r
+ };
\r
+
\r
+ public static final String [] WRITEABLE_FORMATS = new String[]
\r
+ {
\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
\r
+ };
\r
+
\r
\r
public static String INVALID_CHARACTERS = "Contains invalid characters";
\r
\r
public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
\r
"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
\r
\r
\r
public static String INVALID_CHARACTERS = "Contains invalid characters";
\r
\r
public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
\r
"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
\r
\r
- static
\r
- {
\r
- formats.addElement("BLC");
\r
- formats.addElement("CLUSTAL");
\r
- formats.addElement("FASTA");
\r
- formats.addElement("MSF");
\r
- formats.addElement("PileUp");
\r
- formats.addElement("PIR");
\r
- formats.addElement("PFAM");
\r
- formats.addElement("STH");
\r
- formats.addElement("PDB");
\r
- }
\r
-
\r
\r
public static String FILE = "File";
\r
public static String URL = "URL";
\r
\r
public static String FILE = "File";
\r
public static String URL = "URL";
\r
@@
-62,6
+58,16
@@
AlignFile afile = null;
\r
String inFile;
\r
\r
AlignFile afile = null;
\r
String inFile;
\r
\r
+ public static final boolean isValidFormat(String format)
\r
+ {
\r
+ boolean valid = false;
\r
+ for(int i=0; i<READABLE_FORMATS.length; i++)
\r
+ if(READABLE_FORMATS[i].equalsIgnoreCase(format))
\r
+ return true;
\r
+
\r
+ return valid;
\r
+ }
\r
+
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
0fc4aa8
..
10e0bf8
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-138,7
+138,7
@@
public class FileLoader
{
\r
String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
\r
\r
{
\r
String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
\r
\r
- if (FormatAdapter.formats.contains(format))
\r
+ if (FormatAdapter.isValidFormat(format))
\r
{
\r
try
\r
{
\r
{
\r
try
\r
{
\r
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
496585b
..
1b03e19
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-148,11
+148,10
@@
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()-2; i++)
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
{
\r
{
\r
- JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
\r
- elementAt(
\r
- i));
\r
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
\r
+
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
item.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
diff --git
a/src/jalview/ws/JPredClient.java
b/src/jalview/ws/JPredClient.java
index
08d7271
..
ec3f737
100755
(executable)
--- a/
src/jalview/ws/JPredClient.java
+++ b/
src/jalview/ws/JPredClient.java
@@
-406,7
+406,7
@@
public class JPredClient
String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),
\r
"Paste");
\r
\r
String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),
\r
"Paste");
\r
\r
- if (jalview.io.FormatAdapter.formats.contains(format))
\r
+ if (jalview.io.FormatAdapter.isValidFormat(format))
\r
{
\r
al = new Alignment(new FormatAdapter().readFile(
\r
result.getAligfile(), "Paste", format));
\r
{
\r
al = new Alignment(new FormatAdapter().readFile(
\r
result.getAligfile(), "Paste", format));
\r