git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
8f8e686
)
JAL-1775 FileLoader javadoc
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 Jun 2015 13:03:07 +0000
(14:03 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 Jun 2015 13:03:07 +0000
(14:03 +0100)
src/jalview/io/FileLoader.java
patch
|
blob
|
history
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
76bd572
..
0cd2987
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-20,12
+20,6
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
import jalview.api.ComplexAlignFile;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.api.ComplexAlignFile;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
@@
-39,6
+33,12
@@
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
public class FileLoader implements Runnable
{
String file;
public class FileLoader implements Runnable
{
String file;
@@
-317,6
+317,7
@@
public class FileLoader implements Runnable
if ((al != null) && (al.getHeight() > 0))
{
if ((al != null) && (al.getHeight() > 0))
{
+ // construct and register dataset sequences
for (SequenceI sq : al.getSequences())
{
while (sq.getDatasetSequence() != null)
for (SequenceI sq : al.getSequences())
{
while (sq.getDatasetSequence() != null)
@@
-327,13
+328,17
@@
public class FileLoader implements Runnable
{
for (PDBEntry pdbe : sq.getPDBId())
{
{
for (PDBEntry pdbe : sq.getPDBId())
{
+ // register PDB entries with desktop's structure selection
+ // manager
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(pdbe);
}
}
}
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(pdbe);
}
}
}
+
if (viewport != null)
{
if (viewport != null)
{
+ // append to existing alignment
viewport.addAlignment(al, title);
}
else
viewport.addAlignment(al, title);
}
else
@@
-351,8
+356,7
@@
public class FileLoader implements Runnable
ColourSchemeI cs = ((ComplexAlignFile) source)
.getColourScheme();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
ColourSchemeI cs = ((ComplexAlignFile) source)
.getColourScheme();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
alignFrame.getViewport().setShowSequenceFeatures(
showSeqFeatures);
alignFrame.getViewport().setShowSequenceFeatures(
showSeqFeatures);