X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=a95dd273d068454e61aae551f50e95005eb2b191;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=71e9f4eb9c9e3556524ff2476bdb1cdfbd51d280;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 71e9f4e..a95dd27 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -6,29 +6,44 @@
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
MouseListener, SequenceListener
@@ -144,7 +159,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
@@ -237,7 +252,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
@@ -343,35 +358,41 @@ public class SeqPanel extends Panel implements MouseMotionListener,
keyboardNo1.append(value);
}
}
+
int getKeyboardNo1()
{
- try {
- if (keyboardNo1 != null)
+ try
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
- }
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo1 = null;
return 1;
}
int getKeyboardNo2()
{
- try {
- if (keyboardNo2!=null){
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
- }
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo2 = null;
return 1;
}
-
+
void setStatusMessage(SequenceI sequence, int res, int seq)
{
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
@@ -639,7 +660,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
+ {
ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
@@ -689,7 +712,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+ sequence.getName());
@@ -792,19 +817,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
for (int i = 0; i < features.length; i++)
{
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
+ if (av.getFeaturesDisplayed() == null
+ || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
{
continue;
}
if (features[i].featureGroup != null
- && seqCanvas.fr.featureGroups != null
- && seqCanvas.fr.featureGroups
- .containsKey(features[i].featureGroup)
- && !((Boolean) seqCanvas.fr.featureGroups
- .get(features[i].featureGroup)).booleanValue())
+ && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
+ {
continue;
+ }
if ((features[i].getBegin() <= res)
&& (features[i].getEnd() >= res))
@@ -929,7 +952,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.getRepresentedSequences(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
@@ -937,15 +960,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append("Edit group:");
+ message.append(MessageManager.getString("action.edit_group")).append(":");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append("Edit sequence: " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
@@ -953,7 +976,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
@@ -1155,7 +1178,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
startres, startres - lastres, av.getAlignment(), true);
}
}
@@ -1171,7 +1194,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
startres, lastres - startres, av.getAlignment(), true);
}
@@ -1193,7 +1216,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
@@ -1228,7 +1251,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seq }, startres, max, av.getAlignment(), true);
}
}
@@ -1264,10 +1287,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
av.getAlignment(), true);
}
@@ -1275,10 +1298,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
}
@@ -1303,7 +1326,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{