/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns()
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
+ int maxWidth = av.getAlignment().getWidth();
- while (!av.colSel.isVisible(seqCanvas.cursorX)
+ while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
{
seqCanvas.cursorX = 0;
}
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
{
- seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
{
- seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
}
endEditing();
{
ap.scrollUp(false);
}
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
- SequenceGroup sg = av.selectionGroup;
+ SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ int min = av.getAlignment().getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
- int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
if (index > max)
{
max = index;
else
{
// Now add any sequences between min and max
- sg.getSequences(null).removeAllElements();
+ sg.clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
int getKeyboardNo1()
{
- if (keyboardNo1 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
}
+ keyboardNo1 = null;
+ return 1;
}
int getKeyboardNo2()
{
- if (keyboardNo2 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
}
+ keyboardNo2 = null;
+ return 1;
}
void setStatusMessage(SequenceI sequence, int res, int seq)
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1
+ if (av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() == 1
&& av.getSelectionGroup().getEndRes()
- av.getSelectionGroup().getStartRes() < 2)
{
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
if (seq < 0)
{
seq = -1;
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ .getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
{
String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
+ {
ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
ap.alignFrame.statusBar.setText(text.toString());
StringBuffer tooltipText = new StringBuffer();
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
.containsKey(features[i].featureGroup)
&& !((Boolean) seqCanvas.fr.featureGroups
.get(features[i].featureGroup)).booleanValue())
+ {
continue;
+ }
if ((features[i].getBegin() <= res)
&& (features[i].getEnd() >= res))
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
- if (!groupEditing && av.hasHiddenRows)
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
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)
{
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
// Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences)
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
// but the sequence represents a group
if (sg == null)
{
- if (av.hiddenRepSequences == null
- || !av.hiddenRepSequences.containsKey(seq))
+ if (!av.isHiddenRepSequence(seq))
{
endEditing();
return;
}
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
}
fixedLeft = sg.getStartRes();
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
- int g, groupSize = vseqs.size();
- SequenceI[] groupSeqs = new SequenceI[groupSize];
- for (g = 0; g < groupSeqs.length; g++)
- {
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
- }
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
+ .toArray(new SequenceI[0]);
// drag to right
if (insertGap)
// If the user has selected the whole sequence, and is dragging to
// the right, we can still extend the alignment and selectionGroup
if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
- && sg.getEndRes() == av.alignment.getWidth() - 1)
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
{
blank = true;
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
- .getCharAt(fixedRight - j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+ - j)))
{
blank = false;
break;
if (!blank)
{
- if (sg.getSize() == av.alignment.getHeight())
+ if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns && startres < av.getColumnSelection()
- .getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av
+ .getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
- int alWidth = av.alignment.getWidth();
- if (av.hasHiddenRows)
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
{
- int hwidth = av.alignment.getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
// / Are we able to delete?
// ie are all columns blank?
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = startres; j < lastres; j++)
{
- if (groupSeqs[g].getLength() <= j)
+ if (gs.getLength() <= j)
{
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
+ startres, startres - lastres, av.getAlignment(), true);
}
}
else
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
+ startres, lastres - startres, av.getAlignment(), true);
}
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
else
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
+ { seq }, startres, max, av.getAlignment(), true);
}
}
}
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
- true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
+ av.getAlignment(), true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
- true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
+ av.getAlignment(), true);
}
// ////////////////////////////////////////
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if (stretchGroup != null && res > stretchGroup.getStartRes()
&& res < stretchGroup.getEndRes())
{
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
return;
}
+ stretchGroup.recalcConservation(); // always do this - annotation has own
+ // state
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.hiddenRepSequences),
- stretchGroup.getWidth());
- }
-
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
- }
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
- stretchGroup.recalcConservation();
}
else
{
mouseDragging = true;
- if (y > av.alignment.getHeight())
+ if (y > av.getAlignment().getHeight())
{
- y = av.alignment.getHeight() - 1;
+ y = av.getAlignment().getHeight() - 1;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ while ((y != oldSeq) && (oldSeq > -1)
+ && (y < av.getAlignment().getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
}
if (mouseDragging && evt.getY() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
running = ap.scrollUp(false);
}
// rules are: colsel is copied if there is a real intersection between
// sequence selection
boolean repaint = false, copycolsel = true;
- if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
{
SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize()>0)
+ if (seqsel != null && seqsel.getSize() > 0)
{
- if (av.alignment == null)
+ if (av.getAlignment() == null)
{
System.out
.println("Selection message: alignviewport av SeqSetId="
+ " 's alignment is NULL! returning immediatly.");
return;
}
- sgroup = seqsel.intersect(av.alignment,
- (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
if ((sgroup == null || sgroup.getSize() == 0)
&& (colsel == null || colsel.size() == 0))
{
{
av.setSelectionGroup(null);
}
- repaint = av.isSelectionGroupChanged();
+ repaint = av.isSelectionGroupChanged(true);
}
- if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+ if (copycolsel
+ && (av.getColumnSelection() == null || !av
+ .isColSelChanged(true)))
{
// the current selection is unset or from a previous message
// so import the new colsel.
if (colsel == null || colsel.size() == 0)
{
- if (av.colSel != null)
+ if (av.getColumnSelection() != null)
{
- av.colSel.clear();
+ av.getColumnSelection().clear();
}
}
else
{
// TODO: shift colSel according to the intersecting sequences
- if (av.colSel == null)
+ if (av.getColumnSelection() == null)
{
- av.colSel = new ColumnSelection(colsel);
+ av.setColumnSelection(new ColumnSelection(colsel));
}
else
{
- av.colSel.setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel);
}
}
- repaint |= av.isColSelChanged();
+ repaint |= av.isColSelChanged(true);
}
- if (copycolsel && av.hasHiddenColumns
- && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .getHiddenColumns() == null))
{
System.err.println("Bad things");
}
/**
* scroll to the given row/column - or nearest visible location
+ *
* @param row
* @param column
*/
public void scrollTo(int row, int column)
{
-
- row = row<0 ? ap.av.startSeq : row;
- column = column<0 ? ap.av.startRes : column;
- ap.scrollTo(row, row, column, true, true);
+
+ row = row < 0 ? ap.av.startSeq : row;
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, row, true, true);
}
+
/**
* scroll to the given row - or nearest visible location
+ *
* @param row
*/
public void scrollToRow(int row)
{
-
- row = row<0 ? ap.av.startSeq : row;
- ap.scrollTo(row, row, ap.av.startRes, true, true);
+
+ row = row < 0 ? ap.av.startSeq : row;
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
}
+
/**
* scroll to the given column - or nearest visible location
+ *
* @param column
*/
public void scrollToColumn(int column)
{
-
- column = column<0 ? ap.av.startRes : column;
- ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, ap.av.startSeq, true, true);
}
}
git://source.jalview.org / jalview.git / blobdiff