X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=def4be1889ce022c8cc387a5cfc42bf01ef2dc54;hb=4bf989253d9dfaaf960a7522e7b4841eb5fe6f84;hp=893ce2c41f253ec318777ebe2e1dcb629ab3018d;hpb=45709c18006e1fba002a9234a5875c986ae98996;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
old mode 100755
new mode 100644
index 893ce2c..def4be1
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,1787 +1,2801 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.structure.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SeqPanel
- extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener
-
-{
- /** DOCUMENT ME!! */
- public SeqCanvas seqCanvas;
-
- /** DOCUMENT ME!! */
- public AlignmentPanel ap;
- protected int lastres;
- protected int startseq;
- protected AlignViewport av;
-
- ScrollThread scrollThread = null;
- boolean mouseDragging = false;
- boolean editingSeqs = false;
- boolean groupEditing = false;
-
- //////////////////////////////////////////
- /////Everything below this is for defining the boundary of the rubberband
- //////////////////////////////////////////
- int oldSeq = -1;
- boolean changeEndSeq = false;
- boolean changeStartSeq = false;
- boolean changeEndRes = false;
- boolean changeStartRes = false;
- SequenceGroup stretchGroup = null;
- boolean remove = false;
-
- Point lastMousePress;
- boolean mouseWheelPressed = false;
- StringBuffer keyboardNo1;
- StringBuffer keyboardNo2;
-
- java.net.URL linkImageURL;
-
- StringBuffer tooltipText = new StringBuffer("");
- String tmpString;
-
- EditCommand editCommand;
-
- StructureSelectionManager ssm;
-
-
- /**
- * Creates a new SeqPanel object.
- *
- * @param avp DOCUMENT ME!
- * @param p DOCUMENT ME!
- */
- public SeqPanel(AlignViewport av, AlignmentPanel ap)
- {
- linkImageURL = getClass().getResource("/images/link.gif");
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- this.av = av;
- setBackground(Color.white);
-
- seqCanvas = new SeqCanvas(ap);
- setLayout(new BorderLayout());
- add(seqCanvas, BorderLayout.CENTER);
-
- this.ap = ap;
-
- if (!av.isDataset())
- {
- addMouseMotionListener(this);
- addMouseListener(this);
- addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
- ssm.addStructureViewerListener(this);
- }
- }
-
- int startWrapBlock = -1;
- int wrappedBlock = -1;
- int findRes(MouseEvent evt)
- {
- int res = 0;
- int x = evt.getX();
-
- if (av.wrapAlignment)
- {
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- {
- hgap += av.charHeight;
- }
-
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
-
- int y = evt.getY();
- y -= hgap;
- x -= seqCanvas.LABEL_WEST;
-
- int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
- if (cwidth < 1)
- {
- return 0;
- }
-
- wrappedBlock = y / cHeight;
- wrappedBlock += av.getStartRes() / cwidth;
-
- res = wrappedBlock * cwidth + x / av.getCharWidth();
-
- }
- else
- {
- res = (x / av.getCharWidth()) + av.getStartRes();
- }
-
- if (av.hasHiddenColumns)
- {
- res = av.getColumnSelection().adjustForHiddenColumns(res);
- }
-
- return res;
-
- }
-
- int findSeq(MouseEvent evt)
- {
- int seq = 0;
- int y = evt.getY();
-
- if (av.wrapAlignment)
- {
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- {
- hgap += av.charHeight;
- }
-
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
-
- y -= hgap;
-
- seq = Math.min( (y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
- }
- else
- {
- seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
- }
-
- return seq;
- }
-
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
- {
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(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())
- continue;
-
-
- if ( (features[i].getBegin() <= res) &&
- (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
- }
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
- }
-
-
- void endEditing()
- {
- if (editCommand != null && editCommand.getSize() > 0)
- {
- ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null,
- av.getAlignment().getSequences());
- }
-
- startseq = -1;
- lastres = -1;
- editingSeqs = false;
- groupEditing = false;
- keyboardNo1 = null;
- keyboardNo2 = null;
- editCommand = null;
- }
-
- void setCursorRow()
- {
- seqCanvas.cursorY = getKeyboardNo1() - 1;
- scrollToVisible();
- }
-
- void setCursorColumn()
- {
- seqCanvas.cursorX = getKeyboardNo1() - 1;
- scrollToVisible();
- }
-
- void setCursorRowAndColumn()
- {
- if (keyboardNo2 == null)
- {
- keyboardNo2 = new StringBuffer();
- }
- else
- {
- seqCanvas.cursorX = getKeyboardNo1() - 1;
- seqCanvas.cursorY = getKeyboardNo2() - 1;
- scrollToVisible();
- }
- }
-
- void setCursorPosition()
- {
- SequenceI sequence =
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
- seqCanvas.cursorX = sequence.findIndex(
- getKeyboardNo1() - 1
- );
- scrollToVisible();
- }
-
- void moveCursor(int dx, int dy)
- {
- seqCanvas.cursorX += dx;
- seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
- {
- int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
-
- while (!av.colSel.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth
- && seqCanvas.cursorX > 0)
- {
- seqCanvas.cursorX += dx;
- }
-
- if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
- {
- seqCanvas.cursorX = original;
- }
- }
-
- scrollToVisible();
- }
-
- void scrollToVisible()
- {
- if (seqCanvas.cursorX < 0)
- {
- seqCanvas.cursorX = 0;
- }
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
- {
- seqCanvas.cursorX = av.alignment.getWidth() - 1;
- }
-
- if (seqCanvas.cursorY < 0)
- {
- seqCanvas.cursorY = 0;
- }
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
- {
- seqCanvas.cursorY = av.alignment.getHeight() - 1;
- }
-
- endEditing();
- if (av.wrapAlignment)
- {
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
- }
- else
- {
- while (seqCanvas.cursorY < av.startSeq)
- {
- ap.scrollUp(true);
- }
- while (seqCanvas.cursorY + 1 > av.endSeq)
- {
- ap.scrollUp(false);
- }
- if (!av.wrapAlignment)
- {
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
- {
- if (!ap.scrollRight(false))
- {
- break;
- }
- }
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
- {
- if (!ap.scrollRight(true))
- {
- break;
- }
- }
- }
- }
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
- seqCanvas.cursorX, seqCanvas.cursorY);
-
- seqCanvas.repaint();
- }
-
- void setSelectionAreaAtCursor(boolean topLeft)
- {
- SequenceI sequence =
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
- if (av.getSelectionGroup() != null)
- {
- SequenceGroup sg = av.selectionGroup;
- //Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
- for (int i = 0; i < sg.getSize(); i++)
- {
- int index = av.alignment.findIndex(sg.getSequenceAt(i));
- if (index > max)
- {
- max = index;
- }
- if (index < min)
- {
- min = index;
- }
- }
-
- max++;
-
- if (topLeft)
- {
- sg.setStartRes(seqCanvas.cursorX);
- if (sg.getEndRes() < seqCanvas.cursorX)
- {
- sg.setEndRes(seqCanvas.cursorX);
- }
-
- min = seqCanvas.cursorY;
- }
- else
- {
- sg.setEndRes(seqCanvas.cursorX);
- if (sg.getStartRes() > seqCanvas.cursorX)
- {
- sg.setStartRes(seqCanvas.cursorX);
- }
-
- max = seqCanvas.cursorY + 1;
- }
-
- if (min > max)
- {
- // Only the user can do this
- av.setSelectionGroup(null);
- }
- else
- {
- // Now add any sequences between min and max
- sg.getSequences(null).clear();
- for (int i = min; i < max; i++)
- {
- sg.addSequence(av.alignment.getSequenceAt(i), false);
- }
- }
- }
-
- if (av.getSelectionGroup() == null)
- {
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(seqCanvas.cursorX);
- sg.setEndRes(seqCanvas.cursorX);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- }
-
- ap.paintAlignment(false);
- }
-
- void insertGapAtCursor(boolean group)
- {
- groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
- editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
- endEditing();
- }
-
- void deleteGapAtCursor(boolean group)
- {
- groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX + getKeyboardNo1();
- editSequence(false, seqCanvas.cursorX);
- endEditing();
- }
-
- void numberPressed(char value)
- {
- if (keyboardNo1 == null)
- {
- keyboardNo1 = new StringBuffer();
- }
-
- if (keyboardNo2 != null)
- {
- keyboardNo2.append(value);
- }
- else
- {
- keyboardNo1.append(value);
- }
- }
-
- int getKeyboardNo1()
- {
- if (keyboardNo1 == null)
- return 1;
- else
- {
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
- }
- }
-
- int getKeyboardNo2()
- {
- if (keyboardNo2 == null)
- return 1;
- else
- {
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- mouseDragging = false;
- mouseWheelPressed = false;
-
- if (!editingSeqs)
- {
- doMouseReleasedDefineMode(evt);
- return;
- }
-
- endEditing();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
- {
- lastMousePress = evt.getPoint();
-
- if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
- {
- mouseWheelPressed = true;
- return;
- }
-
- if (evt.isShiftDown() || evt.isAltDown() ||
- evt.isControlDown())
- {
- if (evt.isAltDown() || evt.isControlDown())
- {
- groupEditing = true;
- }
- editingSeqs = true;
- }
- else
- {
- doMousePressedDefineMode(evt);
- return;
- }
-
- int seq = findSeq(evt);
- int res = findRes(evt);
-
- if (seq < 0 || res < 0)
- {
- return;
- }
-
- if ( (seq < av.getAlignment().getHeight()) &&
- (res < av.getAlignment().getSequenceAt(seq).getLength()))
- {
- startseq = seq;
- lastres = res;
- }
- else
- {
- startseq = -1;
- lastres = -1;
- }
-
- return;
- }
-
- String lastMessage;
- public void mouseOverSequence(SequenceI sequence, int index)
- {
- String tmp = sequence.hashCode()+index+"";
- if (lastMessage == null || !lastMessage.equals(tmp))
- ssm.mouseOverSequence(sequence, index);
-
- lastMessage = tmp;
- }
-
-
- public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
- {
- if(av.alignment.findIndex(seq)>-1)
- {
- SearchResults highlight = new SearchResults();
- highlight.addResult(seq,index,index);
- seqCanvas.highlightSearchResults(highlight);
- }
- }
-
- public void updateColours(SequenceI seq, int index)
- {
- System.out.println("update the seqPanel colours");
- //repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- if (editingSeqs)
- {
- // This is because MacOSX creates a mouseMoved
- // If control is down, other platforms will not.
- mouseDragged(evt);
- }
-
- int res = findRes(evt);
- int seq = findSeq(evt);
-
- if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
- {
- return;
- }
-
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
- if (res > sequence.getLength())
- {
- return;
- }
-
- if (ssm != null)
- mouseOverSequence(sequence, sequence.findPosition(res));
-
- setStatusMessage(sequence, res, seq);
-
- tooltipText.setLength(6); // Cuts the buffer back to
-
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
- if (groups != null)
- {
- for (int g = 0; g < groups.length; g++)
- {
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
-
- if (!groups[g].getName().startsWith("JTreeGroup") &&
- !groups[g].getName().startsWith("JGroup"))
- {
- tooltipText.append(groups[g].getName());
- }
-
- if (groups[g].getDescription() != null)
- {
- tooltipText.append(": " + groups[g].getDescription());
- }
- }
- }
- }
-
- // use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
- {
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
-
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].getType().equals("disulfide bond"))
- {
- if (features[i].getBegin() == sequence.findPosition(res)
- || features[i].getEnd() == sequence.findPosition(res))
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
- tooltipText.append("disulfide bond " + features[i].getBegin() +
- ":" +
- features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText.append(" ");
- }
- }
- }
- else
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
-
- tooltipText.append(features[i].getType() + " " +
- features[i].begin);
- if (features[i].begin != features[i].end)
- {
- tooltipText.append(" " + features[i].end);
- }
-
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i].getType()))
- {
- tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- }
- int endTag = tmpString.toUpperCase().indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
- endTag = tmpString.toUpperCase().indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
-
- if (startTag > -1)
- {
- tooltipText.append("; " + tmpString);
- }
- else
- {
- if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
- {
- //The description does not specify html is to
- //be used, so we must remove < > symbols
- tmpString = tmpString.replaceAll("<", "<");
- tmpString = tmpString.replaceAll(">", ">");
-
- tooltipText.append("; ");
- tooltipText.append(tmpString);
-
- }
- else
- {
- tooltipText.append("; " + tmpString);
- }
- }
- }
- if (features[i].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText.append("; (" + features[i].getValue("status") + ")");
- }
- }
-
- if (features[i].links != null)
- {
- tooltipText.append(" ");
- }
-
- }
- }
- }
- }
-
- if (tooltipText.length() == 6) //
- {
- setToolTipText(null);
- }
- else
- {
- tooltipText.append("");
- if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
- setToolTipText(tooltipText.toString());
-
- lastTooltip = tooltipText.toString();
- }
-
- }
- String lastTooltip;
-
- void setStatusMessage(SequenceI sequence, int res, int seq)
- {
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
-
- Object obj = null;
- if (av.alignment.isNucleotide())
- {
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
- "");
- if (obj != null)
- {
- text.append(" Nucleotide: ");
- }
- }
- else
- {
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
- {
- text.append(" Residue: ");
- }
- }
-
- if (obj != null)
- {
-
- if (obj != "")
- {
- text.append(obj + " (" + sequence.findPosition(res) +
- ")");
- }
- }
- ap.alignFrame.statusBar.setText(text.toString());
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- if (mouseWheelPressed)
- {
- int oldWidth = av.charWidth;
-
- //Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.getY())
- > Math.abs(evt.getX() - lastMousePress.getX()))
- {
- int fontSize = av.font.getSize();
-
- if (evt.getY() < lastMousePress.getY())
- {
- fontSize--;
- }
- else if (evt.getY() > lastMousePress.getY())
- {
- fontSize++;
- }
-
- if (fontSize < 1)
- {
- fontSize = 1;
- }
-
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
- ap.fontChanged();
- }
- else
- {
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
- {
- av.charWidth--;
- }
- else if (evt.getX() > lastMousePress.getX())
- {
- av.charWidth++;
- }
-
- ap.paintAlignment(false);
- }
-
- FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
-
- lastMousePress = evt.getPoint();
-
- return;
- }
-
- if (!editingSeqs)
- {
- doMouseDraggedDefineMode(evt);
- return;
- }
-
- int res = findRes(evt);
-
- if (res < 0)
- {
- res = 0;
- }
-
- if ( (lastres == -1) || (lastres == res))
- {
- return;
- }
-
- if ( (res < av.getAlignment().getWidth()) && (res < lastres))
- {
- // dragLeft, delete gap
- editSequence(false, res);
- }
- else
- {
- editSequence(true, res);
- }
-
- mouseDragging = true;
- if (scrollThread != null)
- {
- scrollThread.setEvent(evt);
- }
- }
-
-
-
- synchronized void editSequence(boolean insertGap, int startres)
- {
- int fixedLeft = -1;
- int fixedRight = -1;
- boolean fixedColumns = false;
- SequenceGroup sg = av.getSelectionGroup();
-
- SequenceI seq = av.alignment.getSequenceAt(startseq);
-
- //No group, but the sequence may represent a group
- if (!groupEditing && av.hasHiddenRows)
- {
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
- {
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
- groupEditing = true;
- }
- }
-
- StringBuffer message = new StringBuffer();
- if (groupEditing)
- {
- message.append("Edit group:");
- if (editCommand == null)
- {
- editCommand = new EditCommand("Edit Group");
- }
- }
- else
- {
- message.append("Edit sequence: " + seq.getName());
- String label = seq.getName();
- if (label.length() > 10)
- {
- label = label.substring(0, 10);
- }
- if (editCommand == null)
- {
- editCommand = new EditCommand("Edit " + label);
- }
- }
-
- if (insertGap)
- {
- message.append(" insert ");
- }
- else
- {
- message.append(" delete ");
- }
-
- message.append(Math.abs(startres - lastres) + " gaps.");
- ap.alignFrame.statusBar.setText(message.toString());
-
- //Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
- {
- fixedColumns = true;
-
- //sg might be null as the user may only see 1 sequence,
- //but the sequence represents a group
- if (sg == null)
- {
- if (av.hiddenRepSequences == null
- || !av.hiddenRepSequences.containsKey(seq))
- {
- endEditing();
- return;
- }
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
- }
-
- fixedLeft = sg.getStartRes();
- fixedRight = sg.getEndRes();
-
- if ( (startres < fixedLeft && lastres >= fixedLeft)
- || (startres >= fixedLeft && lastres < fixedLeft)
- || (startres > fixedRight && lastres <= fixedRight)
- || (startres <= fixedRight && lastres > fixedRight))
- {
- endEditing();
- return;
- }
-
- if (fixedLeft > startres)
- {
- fixedRight = fixedLeft - 1;
- fixedLeft = 0;
- }
- else if (fixedRight < startres)
- {
- fixedLeft = fixedRight;
- fixedRight = -1;
- }
- }
-
- if (av.hasHiddenColumns)
- {
- fixedColumns = true;
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
- if ( (insertGap && startres > y1 && lastres < y1)
- || (!insertGap && startres < y2 && lastres > y2))
- {
- endEditing();
- return;
- }
-
- //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
- //Selection spans a hidden region
- if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
- {
- if (startres >= y2)
- {
- fixedLeft = y2;
- }
- else
- {
- fixedRight = y2 - 1;
- }
- }
- }
-
- 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);
- }
-
- // 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.setEndRes(av.alignment.getWidth() + startres - lastres);
- fixedRight = sg.getEndRes();
- }
-
- // Is it valid with fixed columns??
- // Find the next gap before the end
- // of the visible region boundary
- boolean blank = false;
- for (fixedRight = fixedRight;
- fixedRight > lastres;
- fixedRight--)
- {
- blank = true;
-
- for (g = 0; g < groupSize; g++)
- {
- for (int j = 0; j < startres - lastres; j++)
- {
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(fixedRight - j)))
- {
- blank = false;
- break;
- }
- }
- }
- if (blank)
- {
- break;
- }
- }
-
- if (!blank)
- {
- if (sg.getSize() == av.alignment.getHeight())
- {
- if ( (av.hasHiddenColumns
- &&
- startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
- {
- endEditing();
- return;
- }
-
- int alWidth = av.alignment.getWidth();
- if (av.hasHiddenRows)
- {
- int hwidth = av.alignment.getHiddenSequences().getWidth();
- if (hwidth > alWidth)
- {
- alWidth = hwidth;
- }
- }
- //We can still insert gaps if the selectionGroup
- //contains all the sequences
- sg.setEndRes(sg.getEndRes() + startres - lastres);
- fixedRight = alWidth + startres - lastres;
- }
- else
- {
- endEditing();
- return;
- }
- }
- }
-
- // drag to left
- else if (!insertGap)
- {
- /// Are we able to delete?
- // ie are all columns blank?
-
- for (g = 0; g < groupSize; g++)
- {
- for (int j = startres; j < lastres; j++)
- {
- if (groupSeqs[g].getLength() <= j)
- {
- continue;
- }
-
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(j)))
- {
- // Not a gap, block edit not valid
- endEditing();
- return;
- }
- }
- }
- }
-
- if (insertGap)
- {
- // dragging to the right
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j < startres; j++)
- {
- insertChar(j, groupSeqs, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- groupSeqs,
- startres, startres - lastres,
- av.alignment,
- true);
- }
- }
- else
- {
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j > startres; j--)
- {
- deleteChar(startres, groupSeqs, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- groupSeqs,
- startres, lastres - startres,
- av.alignment,
- true);
- }
-
- }
- }
- else /////Editing a single sequence///////////
- {
- if (insertGap)
- {
- // dragging to the right
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j < startres; j++)
- {
- insertChar(j, new SequenceI[]
- {seq}, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- new SequenceI[]
- {seq},
- lastres, startres - lastres,
- av.alignment,
- true);
- }
- }
- else
- {
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j > startres; j--)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
- {
- endEditing();
- break;
- }
- deleteChar(startres, new SequenceI[]
- {seq}, fixedRight);
- }
- }
- else
- {
- //could be a keyboard edit trying to delete none gaps
- int max = 0;
- for (int m = startres; m < lastres; m++)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
- {
- break;
- }
- max++;
- }
-
- if (max > 0)
- {
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- new SequenceI[]
- {seq},
- startres, max,
- av.alignment,
- true);
- }
- }
- }
- }
-
- lastres = startres;
- seqCanvas.repaint();
- }
-
- void insertChar(int j, SequenceI[] seq, int fixedColumn)
- {
- int blankColumn = fixedColumn;
- for (int s = 0; s < seq.length; s++)
- {
- //Find the next gap before the end of the visible region boundary
- //If lastCol > j, theres a boundary after the gap insertion
-
- for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
- {
- if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
- {
- //Theres a space, so break and insert the gap
- break;
- }
- }
-
- if (blankColumn <= j)
- {
- blankColumn = fixedColumn;
- endEditing();
- return;
- }
- }
-
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- blankColumn, 1, av.alignment, true);
-
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- j, 1, av.alignment,
- true);
-
- }
-
- void deleteChar(int j, SequenceI[] seq, int fixedColumn)
- {
-
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- j, 1, av.alignment, true);
-
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- fixedColumn, 1, av.alignment, true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent e)
- {
- if (oldSeq < 0)
- {
- oldSeq = 0;
- }
-
- if (scrollThread != null)
- {
- scrollThread.running = false;
- scrollThread = null;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseExited(MouseEvent e)
- {
- if (av.getWrapAlignment())
- {
- return;
- }
-
- if (mouseDragging)
- {
- scrollThread = new ScrollThread();
- }
- }
-
- public void mouseClicked(MouseEvent evt)
- {
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
- if (evt.getClickCount() > 1)
- {
- if (av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
- {
- av.setSelectionGroup(null);
- }
-
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt))
- );
-
- if (features != null && features.length > 0)
- {
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequence,
- features[0].getBegin(),
- features[0].getEnd());
- seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
- {
- seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[]
- {sequence}, features, false, ap);
-
- seqCanvas.highlightSearchResults(null);
- }
- }
- }
-
- public void mouseWheelMoved(MouseWheelEvent e)
- {
- e.consume();
- if (e.getWheelRotation() > 0)
- {
- ap.scrollUp(false);
- }
- else
- {
- ap.scrollUp(true);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMousePressedDefineMode(MouseEvent evt)
- {
- int res = findRes(evt);
- int seq = findSeq(evt);
- oldSeq = seq;
-
- startWrapBlock = wrappedBlock;
-
- if (av.wrapAlignment && seq > av.alignment.getHeight())
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- if (seq < 0 || res < 0)
- {
- return;
- }
-
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
-
- if ( (sequence == null) || (res > sequence.getLength()))
- {
- return;
- }
-
- stretchGroup = av.getSelectionGroup();
-
- if (stretchGroup == null)
- {
- stretchGroup = av.alignment.findGroup(sequence);
-
- if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
- (res < stretchGroup.getEndRes()))
- {
- av.setSelectionGroup(stretchGroup);
- }
- else
- {
- stretchGroup = null;
- }
- }
- else if (!stretchGroup.getSequences(null).contains(sequence) ||
- (stretchGroup.getStartRes() > res) ||
- (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
-
- if (allGroups != null)
- {
- for (int i = 0; i < allGroups.length; i++)
- {
- if ( (allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
- }
-
- av.setSelectionGroup(stretchGroup);
-
- }
-
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
- {
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(res));
- Vector links = new Vector();
- for (int i = 0; i < allFeatures.length; i++)
- {
- if (allFeatures[i].links != null)
- {
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
- }
- }
-
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
- pop.show(this, evt.getX(), evt.getY());
- return;
- }
-
- if (av.cursorMode)
- {
- seqCanvas.cursorX = findRes(evt);
- seqCanvas.cursorY = findSeq(evt);
- seqCanvas.repaint();
- return;
- }
-
- if (stretchGroup == null)
- {
- //Only if left mouse button do we want to change group sizes
-
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- stretchGroup = sg;
-
- if (av.getConservationSelected())
- {
- SliderPanel.setConservationSlider(ap,
- av.getGlobalColourScheme(),
- "Background");
- }
-
- if (av.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
- }
- if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ( (stretchGroup != null) &&
- (stretchGroup.getStartRes() == res))
- {
- // Edit end res position of selected group
- changeStartRes = true;
- }
- stretchGroup.getWidth();
- }
-
- seqCanvas.repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseReleasedDefineMode(MouseEvent evt)
- {
- if (stretchGroup == null)
- {
- return;
- }
-
- 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();
- }
-
- if (stretchGroup.cs.conservationApplied())
- {
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
- else
- {
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
- }
-
- changeEndRes = false;
- changeStartRes = false;
- stretchGroup = null;
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseDraggedDefineMode(MouseEvent evt)
- {
- int res = findRes(evt);
- int y = findSeq(evt);
-
- if (wrappedBlock != startWrapBlock)
- {
- return;
- }
-
- if (stretchGroup == null)
- {
- return;
- }
-
- if (res >= av.alignment.getWidth())
- {
- res = av.alignment.getWidth() - 1;
- }
-
- if (stretchGroup.getEndRes() == res)
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if (stretchGroup.getStartRes() == res)
- {
- // Edit start res position of selected group
- changeStartRes = true;
- }
-
- if (res < av.getStartRes())
- {
- res = av.getStartRes();
- }
-
- if (changeEndRes)
- {
- if (res > (stretchGroup.getStartRes() - 1))
- {
- stretchGroup.setEndRes(res);
- }
- }
- else if (changeStartRes)
- {
- if (res < (stretchGroup.getEndRes() + 1))
- {
- stretchGroup.setStartRes(res);
- }
- }
-
- int dragDirection = 0;
-
- if (y > oldSeq)
- {
- dragDirection = 1;
- }
- else if (y < oldSeq)
- {
- dragDirection = -1;
- }
-
- while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
- {
- // This routine ensures we don't skip any sequences, as the
- // selection is quite slow.
- Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
- oldSeq += dragDirection;
-
- if (oldSeq < 0)
- {
- break;
- }
-
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
- if (stretchGroup.getSequences(null).contains(nextSeq))
- {
- stretchGroup.deleteSequence(seq, false);
- }
- else
- {
- if (seq != null)
- {
- stretchGroup.addSequence(seq, false);
- }
-
- stretchGroup.addSequence(nextSeq, false);
- }
- }
-
- if (oldSeq < 0)
- {
- oldSeq = -1;
- }
-
- mouseDragging = true;
-
- if (scrollThread != null)
- {
- scrollThread.setEvent(evt);
- }
-
- seqCanvas.repaint();
- }
-
- void scrollCanvas(MouseEvent evt)
- {
- if (evt == null)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- scrollThread = null;
- }
- mouseDragging = false;
- }
- else
- {
- if (scrollThread == null)
- {
- scrollThread = new ScrollThread();
- }
-
- mouseDragging = true;
- scrollThread.setEvent(evt);
- }
-
- }
-
- // this class allows scrolling off the bottom of the visible alignment
- class ScrollThread
- extends Thread
- {
- MouseEvent evt;
- boolean running = false;
-
- public ScrollThread()
- {
- start();
- }
-
- public void setEvent(MouseEvent e)
- {
- evt = e;
- }
-
- public void stopScrolling()
- {
- running = false;
- }
-
- public void run()
- {
- running = true;
-
- while (running)
- {
- if (evt != null)
- {
- if (mouseDragging && (evt.getY() < 0) &&
- (av.getStartSeq() > 0))
- {
- running = ap.scrollUp(true);
- }
-
- if (mouseDragging && (evt.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
- {
- running = ap.scrollUp(false);
- }
-
- if (mouseDragging && (evt.getX() < 0))
- {
- running = ap.scrollRight(false);
- }
- else if (mouseDragging && (evt.getX() >= getWidth()))
- {
- running = ap.scrollRight(true);
- }
- }
-
- try
- {
- Thread.sleep(20);
- }
- catch (Exception ex)
- {
- }
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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
+ * Sequence 3 ID: FER1_SOLLC + * Sequence 5 ID: FER1_PEA Residue: THR (4) + * Sequence 5 ID: FER1_PEA Residue: B (3) + * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2) + *+ * + * @param seqName + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(String seqName, int seqIndex, + char sequenceChar, int residuePos) + { + StringBuilder text = new StringBuilder(32); + + /* + * Sequence number (if known), and sequence name. + */ + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); + text.append("Sequence").append(seqno).append(" ID: ") + .append(seqName); + + String residue = null; + + /* + * Try to translate the display character to residue name (null for gap). + */ + boolean isGapped = Comparison.isGap(sequenceChar); + + if (!isGapped) + { + boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); + if (nucleotide) + { + residue = ResidueProperties.nucleotideName.get(displayChar); + } + else + { + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ("*".equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); + } + text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") + .append(": ").append(residue == null ? displayChar : residue); + + text.append(" (").append(Integer.toString(residuePos)).append(")"); + } + ap.alignFrame.setStatus(text.toString()); + } + + /** + * Set the status bar message to highlight the first matched position in + * search results. + * + * @param results + */ + private void setStatusMessage(SearchResultsI results) + { + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return; + } + SequenceI alignedSeq = al.getSequenceAt(sequenceIndex); + SequenceI ds = alignedSeq.getDatasetSequence(); + for (SearchResultMatchI m : results.getResults()) + { + SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + + if (seq == ds) + { + int start = m.getStart(); + setStatusMessage(alignedSeq.getName(), sequenceIndex, + seq.getCharAt(start - 1), start); + return; + } + } + } + + /** + * {@inheritDoc} + */ + @Override + public void mouseDragged(MouseEvent evt) + { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1) + { + return; + } + + if (mouseWheelPressed) + { + boolean inSplitFrame = ap.av.getCodingComplement() != null; + boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna(); + + int oldWidth = av.getCharWidth(); + + // Which is bigger, left-right or up-down? + if (Math.abs(evt.getY() - lastMousePress.getY()) > Math + .abs(evt.getX() - lastMousePress.getX())) + { + /* + * on drag up or down, decrement or increment font size + */ + int fontSize = av.font.getSize(); + boolean fontChanged = false; + + if (evt.getY() < lastMousePress.getY()) + { + fontChanged = true; + fontSize--; + } + else if (evt.getY() > lastMousePress.getY()) + { + fontChanged = true; + fontSize++; + } + + if (fontSize < 1) + { + fontSize = 1; + } + + if (fontChanged) + { + Font newFont = new Font(av.font.getName(), av.font.getStyle(), + fontSize); + av.setFont(newFont, true); + av.setCharWidth(oldWidth); + ap.fontChanged(); + if (copyChanges) + { + ap.av.getCodingComplement().setFont(newFont, true); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } + } + } + else + { + /* + * on drag left or right, decrement or increment character width + */ + int newWidth = 0; + if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) + { + newWidth = av.getCharWidth() - 1; + av.setCharWidth(newWidth); + } + else if (evt.getX() > lastMousePress.getX()) + { + newWidth = av.getCharWidth() + 1; + av.setCharWidth(newWidth); + } + if (newWidth > 0) + { + ap.paintAlignment(false, false); + if (copyChanges) + { + /* + * need to ensure newWidth is set on cdna, regardless of which + * panel the mouse drag happened in; protein will compute its + * character width as 1:1 or 3:1 + */ + av.getCodingComplement().setCharWidth(newWidth); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } + } + } + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); + + lastMousePress = evt.getPoint(); + + return; + } + + if (!editingSeqs) + { + dragStretchGroup(evt); + return; + } + + int res = pos.column; + + if (res < 0) + { + res = 0; + } + + if ((editLastRes == -1) || (editLastRes == res)) + { + return; + } + + if ((res < av.getAlignment().getWidth()) && (res < editLastRes)) + { + // dragLeft, delete gap + editSequence(false, false, res); + } + else + { + editSequence(true, false, res); + } + + mouseDragging = true; + if (scrollThread != null) + { + scrollThread.setMousePosition(evt.getPoint()); + } + } + + /** + * Edits the sequence to insert or delete one or more gaps, in response to a + * mouse drag or cursor mode command. The number of inserts/deletes may be + * specified with the cursor command, or else depends on the mouse event + * (normally one column, but potentially more for a fast mouse drag). + *
+ * Delete gaps is limited to the number of gaps left of the cursor position + * (mouse drag), or at or right of the cursor position (cursor mode). + *
+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in + * the current selection group. + *
+ * In locked editing mode (with a selection group present), inserts/deletions
+ * within the selection group are limited to its boundaries (and edits outside
+ * the group stop at its border).
+ *
+ * @param insertGap
+ * true to insert gaps, false to delete gaps
+ * @param editSeq
+ * (unused parameter)
+ * @param startres
+ * the column at which to perform the action; the number of columns
+ * affected depends on this.editLastRes
(cursor column
+ * position)
+ */
+ synchronized void editSequence(boolean insertGap, boolean editSeq,
+ final int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+
+ // No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows())
+ {
+ if (av.isHiddenRepSequence(seq))
+ {
+ sg = av.getRepresentedSequences(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuilder message = new StringBuilder(64); // for status bar
+
+ /*
+ * make a name for the edit action, for
+ * status bar message and Undo/Redo menu
+ */
+ String label = null;
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ label = MessageManager.getString("action.edit_group");
+ }
+ else
+ {
+ message.append("Edit sequence: " + seq.getName());
+ label = seq.getName();
+ if (label.length() > 10)
+ {
+ label = label.substring(0, 10);
+ }
+ label = MessageManager.formatMessage("label.edit_params",
+ new String[]
+ { label });
+ }
+
+ /*
+ * initialise the edit command if there is not
+ * already one being extended
+ */
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand(label);
+ }
+
+ if (insertGap)
+ {
+ message.append(" insert ");
+ }
+ else
+ {
+ message.append(" delete ");
+ }
+
+ message.append(Math.abs(startres - editLastRes) + " gaps.");
+ ap.alignFrame.setStatus(message.toString());
+
+ /*
+ * is there a selection group containing the sequence being edited?
+ * if so the boundary of the group is the limit of the edit
+ * (but the edit may be inside or outside the selection group)
+ */
+ boolean inSelectionGroup = sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq);
+ if (groupEditing || inSelectionGroup)
+ {
+ fixedColumns = true;
+
+ // sg might be null as the user may only see 1 sequence,
+ // but the sequence represents a group
+ if (sg == null)
+ {
+ if (!av.isHiddenRepSequence(seq))
+ {
+ endEditing();
+ return;
+ }
+ sg = av.getRepresentedSequences(seq);
+ }
+
+ fixedLeft = sg.getStartRes();
+ fixedRight = sg.getEndRes();
+
+ if ((startres < fixedLeft && editLastRes >= fixedLeft)
+ || (startres >= fixedLeft && editLastRes < fixedLeft)
+ || (startres > fixedRight && editLastRes <= fixedRight)
+ || (startres <= fixedRight && editLastRes > fixedRight))
+ {
+ endEditing();
+ return;
+ }
+
+ if (fixedLeft > startres)
+ {
+ fixedRight = fixedLeft - 1;
+ fixedLeft = 0;
+ }
+ else if (fixedRight < startres)
+ {
+ fixedLeft = fixedRight;
+ fixedRight = -1;
+ }
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ fixedColumns = true;
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(true, startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(false, startres);
+
+ if ((insertGap && startres > y1 && editLastRes < y1)
+ || (!insertGap && startres < y2 && editLastRes > y2))
+ {
+ endEditing();
+ return;
+ }
+
+ // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ // Selection spans a hidden region
+ if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+ {
+ if (startres >= y2)
+ {
+ fixedLeft = y2;
+ }
+ else
+ {
+ fixedRight = y2 - 1;
+ }
+ }
+ }
+
+ boolean success = doEditSequence(insertGap, editSeq, startres,
+ fixedRight, fixedColumns, sg);
+
+ /*
+ * report what actually happened (might be less than
+ * what was requested), by inspecting the edit commands added
+ */
+ String msg = getEditStatusMessage(editCommand);
+ ap.alignFrame.setStatus(msg == null ? " " : msg);
+ if (!success)
+ {
+ endEditing();
+ }
+
+ editLastRes = startres;
+ seqCanvas.repaint();
+ }
+
+ /**
+ * A helper method that performs the requested editing to insert or delete
+ * gaps (if possible). Answers true if the edit was successful, false if could
+ * only be performed in part or not at all. Failure may occur in 'locked edit'
+ * mode, when an insertion requires a matching gapped position (or column) to
+ * delete, and deletion requires an adjacent gapped position (or column) to
+ * remove.
+ *
+ * @param insertGap
+ * true if inserting gap(s), false if deleting
+ * @param editSeq
+ * (unused parameter, currently always false)
+ * @param startres
+ * the column at which to perform the edit
+ * @param fixedRight
+ * fixed right boundary column of a locked edit (within or to the
+ * left of a selection group)
+ * @param fixedColumns
+ * true if this is a locked edit
+ * @param sg
+ * the sequence group (if group edit is being performed)
+ * @return
+ */
+ protected boolean doEditSequence(final boolean insertGap,
+ final boolean editSeq, final int startres, int fixedRight,
+ final boolean fixedColumns, final SequenceGroup sg)
+ {
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+ SequenceI[] seqs = new SequenceI[] { seq };
+
+ if (groupEditing)
+ {
+ List