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Correct title for sequence parameter applets
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceFetcher.java
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
f973fbb
..
f3d8e29
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-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
@@
-327,17
+327,18
@@
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
+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
@@
-383,11
+384,6
@@
public class SequenceFetcher
AlignFrame.NEW_WINDOW_WIDTH,
\r
AlignFrame.NEW_WINDOW_HEIGHT);
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
AlignFrame.NEW_WINDOW_WIDTH,
\r
AlignFrame.NEW_WINDOW_HEIGHT);
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
- if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
\r
- {
\r
- af.wrapMenuItem.setSelected(true);
\r
- af.wrapMenuItem_actionPerformed(null);
\r
- }
\r
\r
try
\r
{
\r
\r
try
\r
{
\r