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Remove variables not used
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceFetcher.java
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
75e69c2
..
2beb3d9
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-250,8
+250,8
@@
public class SequenceFetcher
EBIFetchClient ebi = new EBIFetchClient();
\r
File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
\r
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
\r
\r
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
\r
- Vector entries = sff.getUniprotEntries(file);
\r
+ DBRefFetcher dbref = new DBRefFetcher();
\r
+ Vector entries = dbref.getUniprotEntries(file);
\r
\r
if (entries != null)
\r
{
\r
\r
if (entries != null)
\r
{
\r
@@
-301,6
+301,17
@@
public class SequenceFetcher
onlyPdbEntries.addElement(pdb);
\r
}
\r
\r
onlyPdbEntries.addElement(pdb);
\r
}
\r
\r
+ Enumeration en2 = entry.getAccession().elements();
\r
+ while (en2.hasMoreElements())
\r
+ {
\r
+ sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
\r
+ "0",
\r
+ en2.nextElement().toString()));
\r
+ }
\r
+
\r
+
\r
+
\r
+
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
\r
if (entry.getFeature() != null)
\r
{
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
\r
if (entry.getFeature() != null)
\r
{
\r
@@
-327,17
+338,18
@@
public class SequenceFetcher
}
\r
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
}
\r
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
\r
- if (reply == null)
\r
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
\r
+ if (file == null)
\r
return null;
\r
try
\r
{
\r
return null;
\r
try
\r
{
\r
- PDBfile pdbfile = new PDBfile(reply);
\r
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
\r
for (int i = 0; i < pdbfile.chains.size(); i++)
\r
{
\r
if (chain == null ||
\r
( (PDBChain) pdbfile.chains.elementAt(i)).id.
\r
toUpperCase().equals(chain))
\r
for (int i = 0; i < pdbfile.chains.size(); i++)
\r
{
\r
if (chain == null ||
\r
( (PDBChain) pdbfile.chains.elementAt(i)).id.
\r
toUpperCase().equals(chain))
\r
+
\r
result.append("\n>PDB|" + id + "|" +
\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
getName() +
\r
result.append("\n>PDB|" + id + "|" +
\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
getName() +
\r
@@
-363,7
+375,7
@@
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
@@
-374,14
+386,17
@@
public class SequenceFetcher
{
\r
if (alignFrame == null)
\r
{
\r
{
\r
if (alignFrame == null)
\r
{
\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));
\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences),
\r
+ AlignFrame.DEFAULT_WIDTH,
\r
+ AlignFrame.DEFAULT_HEIGHT
\r
+);
\r
af.currentFileFormat = format;
\r
if(title==null)
\r
title = "Retrieved from " + database.getSelectedItem();
\r
Desktop.addInternalFrame(af,
\r
title,
\r
af.currentFileFormat = format;
\r
if(title==null)
\r
title = "Retrieved from " + database.getSelectedItem();
\r
Desktop.addInternalFrame(af,
\r
title,
\r
- AlignFrame.NEW_WINDOW_WIDTH,
\r
- AlignFrame.NEW_WINDOW_HEIGHT);
\r
+ AlignFrame.DEFAULT_WIDTH,
\r
+ AlignFrame.DEFAULT_HEIGHT);
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
\r
try
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
\r
try
\r