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Endres check for wrap alignment
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
a52481d
..
14bf680
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-35,7
+35,7
@@
import jalview.jbgui.*;
import jalview.schemes.*;
\r
import jalview.ws.*;
\r
import java.awt.dnd.*;
\r
import jalview.schemes.*;
\r
import jalview.ws.*;
\r
import java.awt.dnd.*;
\r
-import jalview.biojava.dasobert.eventmodel.*;
\r
+import org.biojava.dasobert.eventmodel.*;
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-60,15
+60,14
@@
public class AlignFrame
Stack redoList = new Stack();
\r
private int treeCount = 0;
\r
\r
Stack redoList = new Stack();
\r
private int treeCount = 0;
\r
\r
-
\r
/**
\r
/**
\r
- * Creates a new AlignFrame object.
\r
- *
\r
- * @param al DOCUMENT ME!
\r
+ * new alignment window with hidden columns
\r
+ * @param al AlignmentI
\r
+ * @param hiddenColumns ColumnSelection or null
\r
*/
\r
*/
\r
- public AlignFrame(AlignmentI al)
\r
- {
\r
- viewport = new AlignViewport(al);
\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
\r
+
\r
+ viewport = new AlignViewport(al, hiddenColumns);
\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
\r
\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
\r
\r
@@
-140,6
+139,17
@@
public class AlignFrame
\r
}
\r
\r
\r
}
\r
\r
+
\r
+ /**
\r
+ * Creates a new AlignFrame object.
\r
+ *
\r
+ * @param al DOCUMENT ME!
\r
+ */
\r
+ public AlignFrame(AlignmentI al)
\r
+ {
\r
+ this(al, null);
\r
+ }
\r
+
\r
public AlignViewport getViewport()
\r
{
\r
return viewport;
\r
public AlignViewport getViewport()
\r
{
\r
return viewport;
\r
@@
-783,7
+793,6
@@
public class AlignFrame
\r
if (newAlignment)
\r
{
\r
\r
if (newAlignment)
\r
{
\r
- System.out.println(format +" 2");
\r
alignment = new Alignment(sequences);
\r
\r
if(Desktop.jalviewClipboard!=null)
\r
alignment = new Alignment(sequences);
\r
\r
if(Desktop.jalviewClipboard!=null)
\r
@@
-794,7
+803,6
@@
public class AlignFrame
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- System.out.println(format +" 24");
\r
alignment = viewport.getAlignment();
\r
\r
//!newAlignment
\r
alignment = viewport.getAlignment();
\r
\r
//!newAlignment
\r
@@
-857,7
+865,7
@@
public class AlignFrame
for(int i=0; i<hc.size(); i++)
\r
{
\r
int [] region = (int[]) hc.elementAt(i);
\r
for(int i=0; i<hc.size(); i++)
\r
{
\r
int [] region = (int[]) hc.elementAt(i);
\r
- af.viewport.hideColumns(region[0], region[1]+1);
\r
+ af.viewport.hideColumns(region[0], region[1]);
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-1415,7
+1423,7
@@
public class AlignFrame
\r
public void showAllColumns_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void showAllColumns_actionPerformed(ActionEvent e)
\r
{
\r
- viewport.getColumnSelection().revealAllHiddenColumns(viewport);
\r
+ viewport.showAllHiddenColumns();
\r
}
\r
\r
public void hideSelSequences_actionPerformed(ActionEvent e)
\r
}
\r
\r
public void hideSelSequences_actionPerformed(ActionEvent e)
\r
@@
-2199,6
+2207,9
@@
public class AlignFrame
return;
\r
}
\r
\r
return;
\r
}
\r
\r
+ if(viewport.alignment.getHeight()<2)
\r
+ return;
\r
+
\r
tp = new TreePanel(viewport, type, pwType);
\r
}
\r
\r
tp = new TreePanel(viewport, type, pwType);
\r
}
\r
\r
@@
-2287,27
+2298,28
@@
public class AlignFrame
* or just the selected set will be submitted for multiple alignment.
\r
*
\r
*/
\r
* or just the selected set will be submitted for multiple alignment.
\r
*
\r
*/
\r
- private SequenceI[] gatherSequencesForAlignment()
\r
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
\r
{
\r
// Now, check we have enough sequences
\r
{
\r
// Now, check we have enough sequences
\r
- SequenceI[] msa = null;
\r
+ AlignmentView msa = null;
\r
\r
if ( (viewport.getSelectionGroup() != null) &&
\r
(viewport.getSelectionGroup().getSize(false) > 1))
\r
{
\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
\r
if ( (viewport.getSelectionGroup() != null) &&
\r
(viewport.getSelectionGroup().getSize(false) > 1))
\r
{
\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
- SequenceGroup seqs = viewport.getSelectionGroup();
\r
+ /*SequenceGroup seqs = viewport.getSelectionGroup();
\r
int sz;
\r
msa = new SequenceI[sz = seqs.getSize(false)];
\r
\r
for (int i = 0; i < sz; i++)
\r
{
\r
msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
int sz;
\r
msa = new SequenceI[sz = seqs.getSize(false)];
\r
\r
for (int i = 0; i < sz; i++)
\r
{
\r
msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
- }
\r
+ } */
\r
+ msa = viewport.getAlignmentView(true);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- Vector seqs = viewport.getAlignment().getSequences();
\r
+ /*Vector seqs = viewport.getAlignment().getSequences();
\r
\r
if (seqs.size() > 1)
\r
{
\r
\r
if (seqs.size() > 1)
\r
{
\r
@@
-2317,7
+2329,8
@@
public class AlignFrame
{
\r
msa[i] = (SequenceI) seqs.elementAt(i);
\r
}
\r
{
\r
msa[i] = (SequenceI) seqs.elementAt(i);
\r
}
\r
- }
\r
+ }*/
\r
+ msa = viewport.getAlignmentView(false);
\r
}
\r
return msa;
\r
}
\r
}
\r
return msa;
\r
}
\r
@@
-2521,7
+2534,7
@@
public class AlignFrame
{
\r
public void actionPerformed(ActionEvent e)
\r
{
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
{
\r
- SequenceI[] msa = gatherSequencesForAlignment();
\r
+ AlignmentView msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
false, true, viewport.getAlignment().getDataset(), af);
\r
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
false, true, viewport.getAlignment().getDataset(), af);
\r
\r
@@
-2538,7
+2551,7
@@
public class AlignFrame
{
\r
public void actionPerformed(ActionEvent e)
\r
{
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
{
\r
- SequenceI[] msa = gatherSequencesForAlignment();
\r
+ AlignmentView msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
true, true, viewport.getAlignment().getDataset(), af);
\r
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
true, true, viewport.getAlignment().getDataset(), af);
\r
\r