-/*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.api.AlignViewportI;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.SequenceListener;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-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.List;
-import java.util.Vector;
-
-import javax.swing.JPanel;
-
-public class SeqPanel extends JPanel implements MouseMotionListener,
- MouseListener, SequenceListener, SelectionListener
-{
-
- public SeqCanvas seqCanvas;
-
- public AlignmentPanel ap;
-
- protected int lastres;
-
- protected int startseq;
-
- protected AlignViewport av;
-
- // if character is inserted or deleted, we will need to recalculate the
- // conservation
- boolean seqEditOccurred = false;
-
- ScrollThread scrollThread = null;
-
- boolean mouseDragging = false;
-
- boolean editingSeqs = false;
-
- boolean groupEditing = false;
-
- int oldSeq = -1;
-
- boolean changeEndSeq = false;
-
- boolean changeStartSeq = false;
-
- boolean changeEndRes = false;
-
- boolean changeStartRes = false;
-
- SequenceGroup stretchGroup = null;
-
- StringBuffer keyboardNo1;
-
- StringBuffer keyboardNo2;
-
- boolean mouseWheelPressed = false;
-
- Point lastMousePress;
-
- EditCommand editCommand;
-
- StructureSelectionManager ssm;
-
- public SeqPanel(AlignViewport avp, AlignmentPanel p)
- {
- this.av = avp;
-
- seqCanvas = new SeqCanvas(avp);
- setLayout(new BorderLayout());
- add(seqCanvas);
-
- ap = p;
-
- seqCanvas.addMouseMotionListener(this);
- seqCanvas.addMouseListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
- ssm.addStructureViewerListener(this);
- ssm.addSelectionListener(this);
-
- seqCanvas.repaint();
- }
-
- 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 = 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.getColumnSelection().isVisible(seqCanvas.cursorX))
- {
- int original = seqCanvas.cursorX - dx;
- int maxWidth = av.getAlignment().getWidth();
-
- while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
- {
- seqCanvas.cursorX += dx;
- }
-
- if (seqCanvas.cursorX >= maxWidth
- || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
- {
- seqCanvas.cursorX = original;
- }
- }
- scrollToVisible();
- }
-
- void scrollToVisible()
- {
- if (seqCanvas.cursorX < 0)
- {
- seqCanvas.cursorX = 0;
- }
- else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
- {
- seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
- }
-
- if (seqCanvas.cursorY < 0)
- {
- seqCanvas.cursorY = 0;
- }
- else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
- {
- seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
- }
-
- endEditing();
- if (av.getWrapAlignment())
- {
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
- }
- else
- {
- while (seqCanvas.cursorY < av.startSeq)
- {
- ap.scrollUp(true);
- }
- while (seqCanvas.cursorY + 1 > av.endSeq)
- {
- ap.scrollUp(false);
- }
- while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.startRes))
- {
-
- if (!ap.scrollRight(false))
- {
- break;
- }
- }
- while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
- {
- if (!ap.scrollRight(true))
- {
- break;
- }
- }
- }
- setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
- seqCanvas.cursorX, seqCanvas.cursorY);
-
- seqCanvas.repaint();
- }
-
- void setSelectionAreaAtCursor(boolean topLeft)
- {
- SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
- if (av.getSelectionGroup() != null)
- {
- SequenceGroup sg = av.getSelectionGroup();
- // Find the top and bottom of this group
- int min = av.getAlignment().getHeight(), max = 0;
- for (int i = 0; i < sg.getSize(); i++)
- {
- int index = av.getAlignment().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.clear();
- for (int i = min; i < max; i++)
- {
- sg.addSequence(av.getAlignment().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);
- av.sendSelection();
- }
-
- 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()
- {
- try
- {
- 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;
- }
- } catch (Exception x)
- {
- }
- keyboardNo2 = null;
- return 1;
- }
-
- /**
- * Set status message in alignment panel
- *
- * @param sequence
- * aligned sequence object
- * @param res
- * alignment column
- * @param seq
- * index of sequence in alignment
- * @return position of res in sequence
- */
- void setStatusMessage(SequenceI sequence, int res, int seq)
- {
- // TODO remove duplication of identical gui method
- StringBuilder text = new StringBuilder(32);
- String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
-
- String residue = null;
- /*
- * Try to translate the display character to residue name (null for gap).
- */
- final String displayChar = String.valueOf(sequence.getCharAt(res));
- if (av.getAlignment().isNucleotide())
- {
- residue = ResidueProperties.nucleotideName.get(displayChar);
- if (residue != null)
- {
- text.append(" Nucleotide: ").append(residue);
- }
- }
- else
- {
- residue = "X".equalsIgnoreCase(displayChar) ? "X"
- : ResidueProperties.aa2Triplet.get(displayChar);
- if (residue != null)
- {
- text.append(" Residue: ").append(residue);
- }
- }
-
- int pos = -1;
- if (residue != null)
- {
- pos = sequence.findPosition(res);
- text.append(" (").append(Integer.toString(pos)).append(")");
- }
- // Object obj = null;
- // if (av.getAlignment().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());
-
- }
-
- /**
- * Set the status bar message to highlight the first matched position in
- * search results.
- *
- * @param results
- */
- private void setStatusMessage(SearchResults results)
- {
- List<Match> matches = results.getResults();
- if (!matches.isEmpty())
- {
- Match m = matches.get(0);
- SequenceI seq = m.getSequence();
- int sequenceIndex = this.av.getAlignment().findIndex(seq);
-
- /*
- * Convert position in sequence (base 1) to sequence character array index
- * (base 0)
- */
- int start = m.getStart() - 1;
- setStatusMessage(seq, start, sequenceIndex);
- }
- }
-
- public void mousePressed(MouseEvent evt)
- {
- lastMousePress = evt.getPoint();
-
- // For now, ignore the mouseWheel font resizing on Macs
- // As the Button2_mask always seems to be true
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
- && !av.MAC)
- {
- mouseWheelPressed = true;
- return;
- }
-
- if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
- {
- if (evt.isControlDown() || evt.isAltDown())
- {
- 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;
- }
-
- public void mouseClicked(MouseEvent evt)
- {
- SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
- if (evt.getClickCount() > 1)
- {
- if (av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
- {
- av.setSelectionGroup(null);
- }
-
- SequenceFeature[] features = findFeaturesAtRes(sequence,
- 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 mouseReleased(MouseEvent evt)
- {
- mouseDragging = false;
- mouseWheelPressed = false;
- ap.paintAlignment(true);
-
- if (!editingSeqs)
- {
- doMouseReleasedDefineMode(evt);
- return;
- }
-
- endEditing();
-
- }
-
- int startWrapBlock = -1;
-
- int wrappedBlock = -1;
-
- int findRes(MouseEvent evt)
- {
- int res = 0;
- int x = evt.getX();
-
- if (av.getWrapAlignment())
- {
-
- int hgap = av.getCharHeight();
- if (av.getScaleAboveWrapped())
- {
- hgap += av.getCharHeight();
- }
-
- int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
-
- int y = evt.getY();
- y -= hgap;
- x -= seqCanvas.LABEL_WEST;
-
- int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
- 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)
- {
- final int sqnum = findAlRow(evt);
- return (sqnum < 0) ? 0 : sqnum;
- }
-
- /**
- *
- * @param evt
- * @return row in alignment that was selected (or -1 for column selection)
- */
- private int findAlRow(MouseEvent evt)
- {
- int seq = 0;
- int y = evt.getY();
-
- if (av.getWrapAlignment())
- {
- int hgap = av.getCharHeight();
- if (av.getScaleAboveWrapped())
- {
- hgap += av.getCharHeight();
- }
-
- int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap
- + seqCanvas.getAnnotationHeight();
-
- y -= hgap;
-
- 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
- .getAlignment().getHeight() - 1);
- if (seq < 0)
- {
- seq = -1;
- }
- }
-
- return seq;
- }
-
- public void doMousePressed(MouseEvent evt)
- {
-
- int seq = findSeq(evt);
- int res = findRes(evt);
-
- if (seq < av.getAlignment().getHeight()
- && res < av.getAlignment().getSequenceAt(seq).getLength())
- {
- // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
- // Find the residue's position in the sequence (res is the position
- // in the alignment
-
- startseq = seq;
- lastres = res;
- }
- else
- {
- startseq = -1;
- lastres = -1;
- }
-
- return;
- }
-
- String lastMessage;
-
- public void mouseOverSequence(SequenceI sequence, int index, int pos)
- {
- String tmp = sequence.hashCode() + index + "";
- if (lastMessage == null || !lastMessage.equals(tmp))
- {
- ssm.mouseOverSequence(sequence, index, pos, av);
- }
-
- lastMessage = tmp;
- }
-
- public void highlightSequence(SearchResults results)
- {
- if (av.isFollowHighlight())
- {
- if (ap.scrollToPosition(results, true))
- {
- ap.alignFrame.repaint();
- }
- }
- setStatusMessage(results);
- seqCanvas.highlightSearchResults(results);
-
- }
-
- @Override
- public VamsasSource getVamsasSource()
- {
- return this.ap == null ? null : this.ap.av;
- }
-
- public void updateColours(SequenceI seq, int index)
- {
- System.out.println("update the seqPanel colours");
- // repaint();
- }
-
- public void mouseMoved(MouseEvent evt)
- {
- int res = findRes(evt);
- int seq = findSeq(evt);
-
- if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
- {
- if (tooltip != null)
- {
- tooltip.setTip("");
- }
- return;
- }
-
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res > sequence.getLength())
- {
- if (tooltip != null)
- {
- tooltip.setTip("");
- }
- return;
- }
-
- int respos = sequence.findPosition(res);
- if (ssm != null)
- {
- mouseOverSequence(sequence, res, respos);
- }
-
- StringBuilder text = new StringBuilder();
- text.append("Sequence ").append(Integer.toString(seq + 1))
- .append(" ID: ").append(sequence.getName());
-
- String obj = null;
- final String ch = String.valueOf(sequence.getCharAt(res));
- if (av.getAlignment().isNucleotide())
- {
- obj = ResidueProperties.nucleotideName.get(ch);
- if (obj != null)
- {
- text.append(" Nucleotide: ").append(obj);
- }
- }
- else
- {
- obj = "X".equalsIgnoreCase(ch) ? "X"
- : ResidueProperties.aa2Triplet.get(ch);
- if (obj != null)
- {
- text.append(" Residue: ").append(obj);
- }
- }
-
- if (obj != null)
- {
- text.append(" (").append(Integer.toString(respos)).append(")");
- }
-
- ap.alignFrame.statusBar.setText(text.toString());
-
- StringBuilder tooltipText = new StringBuilder();
- SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
- if (groups != null)
- {
- for (int g = 0; g < groups.length; g++)
- {
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
- {
- if (!groups[g].getName().startsWith("JTreeGroup")
- && !groups[g].getName().startsWith("JGroup"))
- {
- tooltipText.append(groups[g].getName()).append(" ");
- }
- if (groups[g].getDescription() != null)
- {
- tooltipText.append(groups[g].getDescription());
- }
- tooltipText.append("\n");
- }
- }
- }
-
- // use aa to see if the mouse pointer is on a
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
-
- int index = 0;
- while (index < allFeatures.length)
- {
- SequenceFeature sf = allFeatures[index];
-
- tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
-
- if (sf.getDescription() != null)
- {
- tooltipText.append(" " + sf.getDescription());
- }
-
- if (sf.getValue("status") != null)
- {
- String status = sf.getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText.append(" (" + sf.getValue("status") + ")");
- }
- }
- tooltipText.append("\n");
-
- index++;
- }
-
- if (tooltip == null)
- {
- tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
- }
- else
- {
- tooltip.setTip(tooltipText.toString());
- }
- }
-
- 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.getFeaturesDisplayed() == null
- || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
- {
- continue;
- }
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
- }
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
- }
-
- Tooltip tooltip;
-
- public void mouseDragged(MouseEvent evt)
- {
- if (mouseWheelPressed)
- {
- int oldWidth = av.getCharWidth();
-
- // Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
- - lastMousePress.x))
- {
- int fontSize = av.font.getSize();
-
- if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
- {
- fontSize--;
- }
- else if (evt.getY() > lastMousePress.y)
- {
- fontSize++;
- }
-
- if (fontSize < 1)
- {
- fontSize = 1;
- }
-
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.setCharWidth(oldWidth);
- }
- else
- {
- if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
- {
- av.setCharWidth(av.getCharWidth() - 1);
- }
- else if (evt.getX() > lastMousePress.x)
- {
- av.setCharWidth(av.getCharWidth() + 1);
- }
-
- if (av.getCharWidth() < 1)
- {
- av.setCharWidth(1);
- }
- }
-
- ap.fontChanged();
-
- FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
-
- lastMousePress = evt.getPoint();
-
- ap.paintAlignment(false);
- ap.annotationPanel.image = null;
- 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.getAlignment().getSequenceAt(startseq);
-
- if (!groupEditing && av.hasHiddenRows())
- {
- if (av.isHiddenRepSequence(seq))
- {
- sg = av.getRepresentedSequences(seq);
- groupEditing = true;
- }
- }
-
- StringBuffer message = new StringBuffer();
- if (groupEditing)
- {
- message.append(MessageManager.getString("action.edit_group")).append(
- ":");
- if (editCommand == null)
- {
- editCommand = new EditCommand(
- MessageManager.getString("action.edit_group"));
- }
- }
- else
- {
- message.append(MessageManager.getString("label.edit_sequence"))
- .append(" " + seq.getName());
- String label = seq.getName();
- if (label.length() > 10)
- {
- label = label.substring(0, 10);
- }
- if (editCommand == null)
- {
- editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[]
- { 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.getHiddenRepSequences())
- .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.isHiddenRepSequence(seq))
- {
- endEditing();
- return;
- }
-
- sg = av.getRepresentedSequences(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)
- {
- 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.getAlignment().getWidth() - 1)
- {
- sg.setEndRes(av.getAlignment().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 (SequenceI gs : groupSeqs)
- {
- for (int j = 0; j < startres - lastres; j++)
- {
- if (!Comparison.isGap(gs.getCharAt(fixedRight
- - j)))
- {
- blank = false;
- break;
- }
- }
- }
- if (blank)
- {
- break;
- }
- }
-
- if (!blank)
- {
- if (sg.getSize() == av.getAlignment().getHeight())
- {
- if ((av.hasHiddenColumns() && startres < av
- .getColumnSelection().getHiddenBoundaryRight(startres)))
- {
- endEditing();
- return;
- }
-
- int alWidth = av.getAlignment().getWidth();
- if (av.hasHiddenRows())
- {
- int hwidth = av.getAlignment().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 (SequenceI gs : groupSeqs)
- {
- for (int j = startres; j < lastres; j++)
- {
- if (gs.getLength() <= j)
- {
- continue;
- }
-
- if (!Comparison.isGap(gs.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(Action.INSERT_GAP, groupSeqs, startres,
- startres - lastres, av.getAlignment(), true);
- }
- }
- else
- {
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j > startres; j--)
- {
- deleteChar(startres, groupSeqs, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
- lastres - startres, av.getAlignment(), 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(Action.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
- }
- }
- else
- {
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j > startres; j--)
- {
- if (!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 (!Comparison.isGap(seq.getCharAt(m)))
- {
- break;
- }
- max++;
- }
-
- if (max > 0)
- {
- editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.getAlignment(), 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 (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(Action.DELETE_GAP, seq, blankColumn, 1,
- av.getAlignment(), true);
-
- editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
- true);
-
- }
-
- void deleteChar(int j, SequenceI[] seq, int fixedColumn)
- {
-
- editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
- true);
-
- editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
- av.getAlignment(), true);
- }
-
- // ////////////////////////////////////////
- // ///Everything below this is for defining the boundary of the rubberband
- // ////////////////////////////////////////
- public void doMousePressedDefineMode(MouseEvent evt)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- scrollThread = null;
- }
-
- int res = findRes(evt);
- int seq = findSeq(evt);
- oldSeq = seq;
- startWrapBlock = wrappedBlock;
-
- if (seq == -1)
- {
- return;
- }
-
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
- if (sequence == null || res > sequence.getLength())
- {
- return;
- }
-
- stretchGroup = av.getSelectionGroup();
-
- if (stretchGroup == null)
- {
- stretchGroup = av.getAlignment().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.getAlignment().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);
- }
-
- // DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
- {
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
-
- Vector<String> links = null;
- if (allFeatures != null)
- {
- for (int i = 0; i < allFeatures.length; i++)
- {
- if (allFeatures[i].links != null)
- {
- if (links == null)
- {
- links = new Vector<String>();
- }
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
- }
- }
- }
- APopupMenu popup = new APopupMenu(ap, null, links);
- this.add(popup);
- popup.show(this, evt.getX(), evt.getY());
- return;
- }
-
- if (av.cursorMode)
- {
- seqCanvas.cursorX = findRes(evt);
- seqCanvas.cursorY = findSeq(evt);
- seqCanvas.repaint();
- return;
- }
-
- // Only if left mouse button do we want to change group sizes
-
- if (stretchGroup == null)
- {
- // 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");
- }
-
- }
- }
-
- public void doMouseReleasedDefineMode(MouseEvent evt)
- {
- if (stretchGroup == null)
- {
- return;
- }
-
- stretchGroup.recalcConservation(); // always do this - annotation has own
- // state
- if (stretchGroup.cs != null)
- {
- stretchGroup.cs.alignmentChanged(stretchGroup,
- av.getHiddenRepSequences());
-
- if (stretchGroup.cs.conservationApplied())
- {
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
- else
- {
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
- }
- changeEndRes = false;
- changeStartRes = false;
- stretchGroup = null;
- PaintRefresher.Refresh(ap, av.getSequenceSetId());
- ap.paintAlignment(true);
- av.sendSelection();
- }
-
- public void doMouseDraggedDefineMode(MouseEvent evt)
- {
- int res = findRes(evt);
- int y = findSeq(evt);
-
- if (wrappedBlock != startWrapBlock)
- {
- return;
- }
-
- if (stretchGroup == null)
- {
- return;
- }
-
- mouseDragging = true;
-
- if (y > av.getAlignment().getHeight())
- {
- y = av.getAlignment().getHeight() - 1;
- }
-
- if (res >= av.getAlignment().getWidth())
- {
- res = av.getAlignment().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 < 0)
- {
- res = 0;
- }
-
- 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.getAlignment().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;
- }
-
- if (res > av.endRes || res < av.startRes || y < av.startSeq
- || y > av.endSeq)
- {
- mouseExited(evt);
- }
-
- if (scrollThread != null)
- {
- scrollThread.setEvent(evt);
- }
-
- seqCanvas.repaint();
- }
-
- public void mouseEntered(MouseEvent e)
- {
- if (oldSeq < 0)
- {
- oldSeq = 0;
- }
-
- if (scrollThread != null)
- {
- scrollThread.running = false;
- scrollThread = null;
- }
- }
-
- public void mouseExited(MouseEvent e)
- {
- if (av.getWrapAlignment())
- {
- return;
- }
-
- if (mouseDragging && scrollThread == null)
- {
- scrollThread = new ScrollThread();
- }
- }
-
- 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() >= getSize().height
- && av.getAlignment().getHeight() > av.getEndSeq())
- {
- running = ap.scrollUp(false);
- }
-
- if (mouseDragging && evt.getX() < 0)
- {
- running = ap.scrollRight(false);
- }
-
- else if (mouseDragging && evt.getX() >= getSize().width)
- {
- running = ap.scrollRight(true);
- }
- }
-
- try
- {
- Thread.sleep(75);
- } catch (Exception ex)
- {
- }
- }
- }
- }
-
- /**
- * modify current selection according to a received message.
- */
- public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
- {
- // TODO: fix this hack - source of messages is align viewport, but SeqPanel
- // handles selection messages...
- // TODO: extend config options to allow user to control if selections may be
- // shared between viewports.
- if (av != null
- && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId()))))
- {
- return;
- }
-
- /*
- * Check for selection in a view of which this one is a dna/protein
- * complement.
- */
- if (selectionFromTranslation(seqsel, colsel, source))
- {
- return;
- }
-
- // do we want to thread this ? (contention with seqsel and colsel locks, I
- // suspect)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
- boolean repaint = false, copycolsel = true;
- if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
- {
- SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize() > 0)
- {
- if (av.getAlignment() == null)
- {
- System.out
- .println("Selection message: alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId="
- + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
- return;
- }
- sgroup = seqsel.intersect(av.getAlignment(),
- (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- && (colsel == null || colsel.size() == 0))
- {
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
- }
- }
- if (sgroup != null && sgroup.getSize() > 0)
- {
- av.setSelectionGroup(sgroup);
- }
- else
- {
- av.setSelectionGroup(null);
- }
- repaint = av.isSelectionGroupChanged(true);
- }
- 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.getColumnSelection() != null)
- {
- av.getColumnSelection().clear();
- }
- }
- else
- {
- // TODO: shift colSel according to the intersecting sequences
- if (av.getColumnSelection() == null)
- {
- av.setColumnSelection(new ColumnSelection(colsel));
- }
- else
- {
- av.getColumnSelection().setElementsFrom(colsel);
- }
- }
- repaint |= av.isColSelChanged(true);
- }
- if (copycolsel
- && av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection()
- .getHiddenColumns() == null))
- {
- System.err.println("Bad things");
- }
- if (repaint)
- {
- ap.scalePanelHolder.repaint();
- ap.repaint();
- }
- }
-
- /**
- * 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(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(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(column, column, ap.av.startSeq, true, true);
- }
-
- /**
- * If this panel is a cdna/protein translation view of the selection source,
- * tries to map the source selection to a local one, and returns true. Else
- * returns false.
- *
- * @param seqsel
- * @param colsel
- * @param source
- */
- protected boolean selectionFromTranslation(SequenceGroup seqsel,
- ColumnSelection colsel, SelectionSource source)
- {
- if (!(source instanceof AlignViewportI)) {
- return false;
- }
- final AlignViewportI sourceAv = (AlignViewportI) source;
- if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
- {
- return false;
- }
-
- /*
- * Map sequence selection
- */
- SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
- av.setSelectionGroup(sg);
- av.isSelectionGroupChanged(true);
-
- /*
- * Map column selection
- */
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
- av);
- av.setColumnSelection(cs);
- av.isColSelChanged(true);
-
- ap.scalePanelHolder.repaint();
- ap.repaint();
-
- return true;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.api.AlignViewportI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.EditCommand.Action;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.SearchResults.Match;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.structure.SelectionListener;\r
+import jalview.structure.SelectionSource;\r
+import jalview.structure.SequenceListener;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.structure.VamsasSource;\r
+import jalview.util.Comparison;\r
+import jalview.util.MappingUtils;\r
+import jalview.util.MessageManager;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Point;\r
+import java.awt.event.InputEvent;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.MouseMotionListener;\r
+import java.util.List;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JPanel;\r
+\r
+public class SeqPanel extends JPanel implements MouseMotionListener,\r
+ MouseListener, SequenceListener, SelectionListener\r
+{\r
+\r
+ public SeqCanvas seqCanvas;\r
+\r
+ public AlignmentPanel ap;\r
+\r
+ protected int lastres;\r
+\r
+ protected int startseq;\r
+\r
+ protected AlignViewport av;\r
+\r
+ // if character is inserted or deleted, we will need to recalculate the\r
+ // conservation\r
+ boolean seqEditOccurred = false;\r
+\r
+ ScrollThread scrollThread = null;\r
+\r
+ boolean mouseDragging = false;\r
+\r
+ boolean editingSeqs = false;\r
+\r
+ boolean groupEditing = false;\r
+\r
+ int oldSeq = -1;\r
+\r
+ boolean changeEndSeq = false;\r
+\r
+ boolean changeStartSeq = false;\r
+\r
+ boolean changeEndRes = false;\r
+\r
+ boolean changeStartRes = false;\r
+\r
+ SequenceGroup stretchGroup = null;\r
+\r
+ StringBuffer keyboardNo1;\r
+\r
+ StringBuffer keyboardNo2;\r
+\r
+ boolean mouseWheelPressed = false;\r
+\r
+ Point lastMousePress;\r
+\r
+ EditCommand editCommand;\r
+\r
+ StructureSelectionManager ssm;\r
+\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ {\r
+ this.av = avp;\r
+\r
+ seqCanvas = new SeqCanvas(avp);\r
+ setLayout(new BorderLayout());\r
+ add(seqCanvas);\r
+\r
+ ap = p;\r
+\r
+ seqCanvas.addMouseMotionListener(this);\r
+ seqCanvas.addMouseListener(this);\r
+ ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);\r
+ ssm.addStructureViewerListener(this);\r
+ ssm.addSelectionListener(this);\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ void endEditing()\r
+ {\r
+ if (editCommand != null && editCommand.getSize() > 0)\r
+ {\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+ av.firePropertyChange("alignment", null, av.getAlignment()\r
+ .getSequences());\r
+ }\r
+\r
+ startseq = -1;\r
+ lastres = -1;\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
+ keyboardNo1 = null;\r
+ keyboardNo2 = null;\r
+ editCommand = null;\r
+ }\r
+\r
+ void setCursorRow()\r
+ {\r
+ seqCanvas.cursorY = getKeyboardNo1() - 1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void setCursorColumn()\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo1() - 1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void setCursorRowAndColumn()\r
+ {\r
+ if (keyboardNo2 == null)\r
+ {\r
+ keyboardNo2 = new StringBuffer();\r
+ }\r
+ else\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo1() - 1;\r
+ seqCanvas.cursorY = getKeyboardNo2() - 1;\r
+ scrollToVisible();\r
+ }\r
+ }\r
+\r
+ void setCursorPosition()\r
+ {\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void moveCursor(int dx, int dy)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ seqCanvas.cursorY += dy;\r
+ if (av.hasHiddenColumns()\r
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))\r
+ {\r
+ int original = seqCanvas.cursorX - dx;\r
+ int maxWidth = av.getAlignment().getWidth();\r
+\r
+ while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)\r
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ }\r
+\r
+ if (seqCanvas.cursorX >= maxWidth\r
+ || !av.getColumnSelection().isVisible(seqCanvas.cursorX))\r
+ {\r
+ seqCanvas.cursorX = original;\r
+ }\r
+ }\r
+ scrollToVisible();\r
+ }\r
+\r
+ void scrollToVisible()\r
+ {\r
+ if (seqCanvas.cursorX < 0)\r
+ {\r
+ seqCanvas.cursorX = 0;\r
+ }\r
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)\r
+ {\r
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;\r
+ }\r
+\r
+ if (seqCanvas.cursorY < 0)\r
+ {\r
+ seqCanvas.cursorY = 0;\r
+ }\r
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)\r
+ {\r
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;\r
+ }\r
+\r
+ endEditing();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
+ }\r
+ else\r
+ {\r
+ while (seqCanvas.cursorY < av.startSeq)\r
+ {\r
+ ap.scrollUp(true);\r
+ }\r
+ while (seqCanvas.cursorY + 1 > av.endSeq)\r
+ {\r
+ ap.scrollUp(false);\r
+ }\r
+ while (seqCanvas.cursorX < av.getColumnSelection()\r
+ .adjustForHiddenColumns(av.startRes))\r
+ {\r
+\r
+ if (!ap.scrollRight(false))\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ while (seqCanvas.cursorX > av.getColumnSelection()\r
+ .adjustForHiddenColumns(av.endRes))\r
+ {\r
+ if (!ap.scrollRight(true))\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),\r
+ seqCanvas.cursorX, seqCanvas.cursorY);\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ void setSelectionAreaAtCursor(boolean topLeft)\r
+ {\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ if (av.getSelectionGroup() != null)\r
+ {\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ // Find the top and bottom of this group\r
+ int min = av.getAlignment().getHeight(), max = 0;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ int index = av.getAlignment().findIndex(sg.getSequenceAt(i));\r
+ if (index > max)\r
+ {\r
+ max = index;\r
+ }\r
+ if (index < min)\r
+ {\r
+ min = index;\r
+ }\r
+ }\r
+\r
+ max++;\r
+\r
+ if (topLeft)\r
+ {\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ if (sg.getEndRes() < seqCanvas.cursorX)\r
+ {\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ }\r
+\r
+ min = seqCanvas.cursorY;\r
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ if (sg.getStartRes() > seqCanvas.cursorX)\r
+ {\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ }\r
+\r
+ max = seqCanvas.cursorY + 1;\r
+ }\r
+\r
+ if (min > max)\r
+ {\r
+ // Only the user can do this\r
+ av.setSelectionGroup(null);\r
+ }\r
+ else\r
+ {\r
+ // Now add any sequences between min and max\r
+ sg.clear();\r
+ for (int i = min; i < max; i++)\r
+ {\r
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.getSelectionGroup() == null)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ }\r
+ ap.paintAlignment(false);\r
+ av.sendSelection();\r
+ }\r
+\r
+ void insertGapAtCursor(boolean group)\r
+ {\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX;\r
+ editSequence(true, seqCanvas.cursorX + getKeyboardNo1());\r
+ endEditing();\r
+ }\r
+\r
+ void deleteGapAtCursor(boolean group)\r
+ {\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX + getKeyboardNo1();\r
+ editSequence(false, seqCanvas.cursorX);\r
+ endEditing();\r
+ }\r
+\r
+ void numberPressed(char value)\r
+ {\r
+ if (keyboardNo1 == null)\r
+ {\r
+ keyboardNo1 = new StringBuffer();\r
+ }\r
+\r
+ if (keyboardNo2 != null)\r
+ {\r
+ keyboardNo2.append(value);\r
+ }\r
+ else\r
+ {\r
+ keyboardNo1.append(value);\r
+ }\r
+ }\r
+\r
+ int getKeyboardNo1()\r
+ {\r
+ try\r
+ {\r
+ if (keyboardNo1 != null)\r
+ {\r
+ int value = Integer.parseInt(keyboardNo1.toString());\r
+ keyboardNo1 = null;\r
+ return value;\r
+ }\r
+ } catch (Exception x)\r
+ {\r
+ }\r
+ keyboardNo1 = null;\r
+ return 1;\r
+ }\r
+\r
+ int getKeyboardNo2()\r
+ {\r
+ try\r
+ {\r
+ if (keyboardNo2 != null)\r
+ {\r
+ int value = Integer.parseInt(keyboardNo2.toString());\r
+ keyboardNo2 = null;\r
+ return value;\r
+ }\r
+ } catch (Exception x)\r
+ {\r
+ }\r
+ keyboardNo2 = null;\r
+ return 1;\r
+ }\r
+\r
+ /**\r
+ * Set status message in alignment panel\r
+ * \r
+ * @param sequence\r
+ * aligned sequence object\r
+ * @param res\r
+ * alignment column\r
+ * @param seq\r
+ * index of sequence in alignment\r
+ * @return position of res in sequence\r
+ */\r
+ void setStatusMessage(SequenceI sequence, int res, int seq)\r
+ {\r
+ // TODO remove duplication of identical gui method\r
+ StringBuilder text = new StringBuilder(32);\r
+ String seqno = seq == -1 ? "" : " " + (seq + 1);\r
+ text.append("Sequence" + seqno + " ID: " + sequence.getName());\r
+\r
+ String residue = null;\r
+ /*\r
+ * Try to translate the display character to residue name (null for gap).\r
+ */\r
+ final String displayChar = String.valueOf(sequence.getCharAt(res));\r
+ if (av.getAlignment().isNucleotide())\r
+ {\r
+ residue = ResidueProperties.nucleotideName.get(displayChar);\r
+ if (residue != null)\r
+ {\r
+ text.append(" Nucleotide: ").append(residue);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"\r
+ : ResidueProperties.aa2Triplet.get(displayChar);\r
+ if (residue != null)\r
+ {\r
+ text.append(" Residue: ").append(residue);\r
+ }\r
+ }\r
+\r
+ int pos = -1;\r
+ if (residue != null)\r
+ {\r
+ pos = sequence.findPosition(res);\r
+ text.append(" (").append(Integer.toString(pos)).append(")");\r
+ }\r
+ // Object obj = null;\r
+ // if (av.getAlignment().isNucleotide())\r
+ // {\r
+ // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)\r
+ // + "");\r
+ // if (obj != null)\r
+ // {\r
+ // text.append(" Nucleotide: ");\r
+ // }\r
+ // }\r
+ // else\r
+ // {\r
+ // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ // if (obj != null)\r
+ // {\r
+ // text.append(" Residue: ");\r
+ // }\r
+ // }\r
+ //\r
+ // if (obj != null)\r
+ // {\r
+ //\r
+ // if (obj != "")\r
+ // {\r
+ // text.append(obj + " (" + sequence.findPosition(res) + ")");\r
+ // }\r
+ // }\r
+\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ }\r
+\r
+ /**\r
+ * Set the status bar message to highlight the first matched position in\r
+ * search results.\r
+ * \r
+ * @param results\r
+ */\r
+ private void setStatusMessage(SearchResults results)\r
+ {\r
+ List<Match> matches = results.getResults();\r
+ if (!matches.isEmpty())\r
+ {\r
+ Match m = matches.get(0);\r
+ SequenceI seq = m.getSequence();\r
+ int sequenceIndex = this.av.getAlignment().findIndex(seq);\r
+\r
+ /*\r
+ * Convert position in sequence (base 1) to sequence character array index\r
+ * (base 0)\r
+ */\r
+ int start = m.getStart() - 1;\r
+ setStatusMessage(seq, start, sequenceIndex);\r
+ }\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ lastMousePress = evt.getPoint();\r
+\r
+ // For now, ignore the mouseWheel font resizing on Macs\r
+ // As the Button2_mask always seems to be true\r
+ if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK\r
+ && !av.MAC)\r
+ {\r
+ mouseWheelPressed = true;\r
+ return;\r
+ }\r
+\r
+ if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())\r
+ {\r
+ if (evt.isControlDown() || evt.isAltDown())\r
+ {\r
+ groupEditing = true;\r
+ }\r
+ editingSeqs = true;\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
+\r
+ if (seq < 0 || res < 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ((seq < av.getAlignment().getHeight())\r
+ && (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
+ {\r
+ startseq = seq;\r
+ lastres = res;\r
+ }\r
+ else\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ }\r
+\r
+ return;\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));\r
+ if (evt.getClickCount() > 1)\r
+ {\r
+ if (av.getSelectionGroup() != null\r
+ && av.getSelectionGroup().getSize() == 1\r
+ && av.getSelectionGroup().getEndRes()\r
+ - av.getSelectionGroup().getStartRes() < 2)\r
+ {\r
+ av.setSelectionGroup(null);\r
+ }\r
+\r
+ SequenceFeature[] features = findFeaturesAtRes(sequence,\r
+ sequence.findPosition(findRes(evt)));\r
+\r
+ if (features != null && features.length > 0)\r
+ {\r
+ SearchResults highlight = new SearchResults();\r
+ highlight.addResult(sequence, features[0].getBegin(),\r
+ features[0].getEnd());\r
+ seqCanvas.highlightSearchResults(highlight);\r
+ }\r
+ if (features != null && features.length > 0)\r
+ {\r
+ seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]\r
+ { sequence }, features, false, ap);\r
+\r
+ seqCanvas.highlightSearchResults(null);\r
+ }\r
+ }\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ mouseDragging = false;\r
+ mouseWheelPressed = false;\r
+ ap.paintAlignment(true);\r
+\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+ endEditing();\r
+\r
+ }\r
+\r
+ int startWrapBlock = -1;\r
+\r
+ int wrappedBlock = -1;\r
+\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+\r
+ int hgap = av.getCharHeight();\r
+ if (av.getScaleAboveWrapped())\r
+ {\r
+ hgap += av.getCharHeight();\r
+ }\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()\r
+ + hgap\r
+ + seqCanvas.getAnnotationHeight();\r
+\r
+ int y = evt.getY();\r
+ y -= hgap;\r
+ x -= seqCanvas.LABEL_WEST;\r
+\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+ if (cwidth < 1)\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ wrappedBlock = y / cHeight;\r
+ wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+ res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
+ }\r
+ else\r
+ {\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
+ }\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\r
+\r
+ return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+ final int sqnum = findAlRow(evt);\r
+ return (sqnum < 0) ? 0 : sqnum;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param evt\r
+ * @return row in alignment that was selected (or -1 for column selection)\r
+ */\r
+ private int findAlRow(MouseEvent evt)\r
+ {\r
+ int seq = 0;\r
+ int y = evt.getY();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int hgap = av.getCharHeight();\r
+ if (av.getScaleAboveWrapped())\r
+ {\r
+ hgap += av.getCharHeight();\r
+ }\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()\r
+ + hgap\r
+ + seqCanvas.getAnnotationHeight();\r
+\r
+ y -= hgap;\r
+\r
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()\r
+ .getHeight() - 1);\r
+ if (seq < 0)\r
+ {\r
+ seq = -1;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av\r
+ .getAlignment().getHeight() - 1);\r
+ if (seq < 0)\r
+ {\r
+ seq = -1;\r
+ }\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
+\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
+\r
+ if (seq < av.getAlignment().getHeight()\r
+ && res < av.getAlignment().getSequenceAt(seq).getLength())\r
+ {\r
+ // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
+ // Find the residue's position in the sequence (res is the position\r
+ // in the alignment\r
+\r
+ startseq = seq;\r
+ lastres = res;\r
+ }\r
+ else\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ }\r
+\r
+ return;\r
+ }\r
+\r
+ String lastMessage;\r
+\r
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)\r
+ {\r
+ String tmp = sequence.hashCode() + index + "";\r
+ if (lastMessage == null || !lastMessage.equals(tmp))\r
+ {\r
+ ssm.mouseOverSequence(sequence, index, pos, av);\r
+ }\r
+\r
+ lastMessage = tmp;\r
+ }\r
+\r
+ public void highlightSequence(SearchResults results)\r
+ {\r
+ if (av.isFollowHighlight())\r
+ {\r
+ if (ap.scrollToPosition(results, true))\r
+ {\r
+ ap.alignFrame.repaint();\r
+ }\r
+ }\r
+ setStatusMessage(results);\r
+ seqCanvas.highlightSearchResults(results);\r
+\r
+ }\r
+\r
+ @Override\r
+ public VamsasSource getVamsasSource()\r
+ {\r
+ return this.ap == null ? null : this.ap.av;\r
+ }\r
+\r
+ public void updateColours(SequenceI seq, int index)\r
+ {\r
+ System.out.println("update the seqPanel colours");\r
+ // repaint();\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
+\r
+ if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)\r
+ {\r
+ if (tooltip != null)\r
+ {\r
+ tooltip.setTip("");\r
+ }\r
+ return;\r
+ }\r
+\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ if (res > sequence.getLength())\r
+ {\r
+ if (tooltip != null)\r
+ {\r
+ tooltip.setTip("");\r
+ }\r
+ return;\r
+ }\r
+\r
+ int respos = sequence.findPosition(res);\r
+ if (ssm != null)\r
+ {\r
+ mouseOverSequence(sequence, res, respos);\r
+ }\r
+\r
+ StringBuilder text = new StringBuilder();\r
+ text.append("Sequence ").append(Integer.toString(seq + 1))\r
+ .append(" ID: ").append(sequence.getName());\r
+\r
+ String obj = null;\r
+ final String ch = String.valueOf(sequence.getCharAt(res));\r
+ if (av.getAlignment().isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(ch);\r
+ if (obj != null)\r
+ {\r
+ text.append(" Nucleotide: ").append(obj);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ obj = "X".equalsIgnoreCase(ch) ? "X"\r
+ : ResidueProperties.aa2Triplet.get(ch);\r
+ if (obj != null)\r
+ {\r
+ text.append(" Residue: ").append(obj);\r
+ }\r
+ }\r
+\r
+ if (obj != null)\r
+ {\r
+ text.append(" (").append(Integer.toString(respos)).append(")");\r
+ }\r
+\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ StringBuilder tooltipText = new StringBuilder();\r
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);\r
+ if (groups != null)\r
+ {\r
+ for (int g = 0; g < groups.length; g++)\r
+ {\r
+ if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)\r
+ {\r
+ if (!groups[g].getName().startsWith("JTreeGroup")\r
+ && !groups[g].getName().startsWith("JGroup"))\r
+ {\r
+ tooltipText.append(groups[g].getName()).append(" ");\r
+ }\r
+ if (groups[g].getDescription() != null)\r
+ {\r
+ tooltipText.append(groups[g].getDescription());\r
+ }\r
+ tooltipText.append("\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ // use aa to see if the mouse pointer is on a\r
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,\r
+ sequence.findPosition(res));\r
+\r
+ int index = 0;\r
+ while (index < allFeatures.length)\r
+ {\r
+ SequenceFeature sf = allFeatures[index];\r
+\r
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);\r
+\r
+ if (sf.getDescription() != null)\r
+ {\r
+ tooltipText.append(" " + sf.getDescription());\r
+ }\r
+\r
+ if (sf.getValue("status") != null)\r
+ {\r
+ String status = sf.getValue("status").toString();\r
+ if (status.length() > 0)\r
+ {\r
+ tooltipText.append(" (" + sf.getValue("status") + ")");\r
+ }\r
+ }\r
+ tooltipText.append("\n");\r
+\r
+ index++;\r
+ }\r
+\r
+ if (tooltip == null)\r
+ {\r
+ tooltip = new Tooltip(tooltipText.toString(), seqCanvas);\r
+ }\r
+ else\r
+ {\r
+ tooltip.setTip(tooltipText.toString());\r
+ }\r
+ }\r
+\r
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)\r
+ {\r
+ Vector tmp = new Vector();\r
+ SequenceFeature[] features = sequence.getSequenceFeatures();\r
+ if (features != null)\r
+ {\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+ if (av.getFeaturesDisplayed() == null\r
+ || !av.getFeaturesDisplayed().isVisible(features[i].getType()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (features[i].featureGroup != null\r
+ && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ((features[i].getBegin() <= res)\r
+ && (features[i].getEnd() >= res))\r
+ {\r
+ tmp.addElement(features[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ features = new SequenceFeature[tmp.size()];\r
+ tmp.copyInto(features);\r
+\r
+ return features;\r
+ }\r
+\r
+ Tooltip tooltip;\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (mouseWheelPressed)\r
+ {\r
+ int oldWidth = av.getCharWidth();\r
+\r
+ // Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()\r
+ - lastMousePress.x))\r
+ {\r
+ int fontSize = av.font.getSize();\r
+\r
+ if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)\r
+ {\r
+ fontSize--;\r
+ }\r
+ else if (evt.getY() > lastMousePress.y)\r
+ {\r
+ fontSize++;\r
+ }\r
+\r
+ if (fontSize < 1)\r
+ {\r
+ fontSize = 1;\r
+ }\r
+\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.setCharWidth(oldWidth);\r
+ }\r
+ else\r
+ {\r
+ if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)\r
+ {\r
+ av.setCharWidth(av.getCharWidth() - 1);\r
+ }\r
+ else if (evt.getX() > lastMousePress.x)\r
+ {\r
+ av.setCharWidth(av.getCharWidth() + 1);\r
+ }\r
+\r
+ if (av.getCharWidth() < 1)\r
+ {\r
+ av.setCharWidth(1);\r
+ }\r
+ }\r
+\r
+ ap.fontChanged();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();\r
+\r
+ lastMousePress = evt.getPoint();\r
+\r
+ ap.paintAlignment(false);\r
+ ap.annotationPanel.image = null;\r
+ return;\r
+ }\r
+\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseDraggedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+ int res = findRes(evt);\r
+\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
+\r
+ if ((lastres == -1) || (lastres == res))\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ((res < av.getAlignment().getWidth()) && (res < lastres))\r
+ {\r
+ // dragLeft, delete gap\r
+ editSequence(false, res);\r
+ }\r
+ else\r
+ {\r
+ editSequence(true, res);\r
+ }\r
+\r
+ mouseDragging = true;\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ }\r
+\r
+ synchronized void editSequence(boolean insertGap, int startres)\r
+ {\r
+ int fixedLeft = -1;\r
+ int fixedRight = -1;\r
+ boolean fixedColumns = false;\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);\r
+\r
+ if (!groupEditing && av.hasHiddenRows())\r
+ {\r
+ if (av.isHiddenRepSequence(seq))\r
+ {\r
+ sg = av.getRepresentedSequences(seq);\r
+ groupEditing = true;\r
+ }\r
+ }\r
+\r
+ StringBuffer message = new StringBuffer();\r
+ if (groupEditing)\r
+ {\r
+ message.append(MessageManager.getString("action.edit_group")).append(\r
+ ":");\r
+ if (editCommand == null)\r
+ {\r
+ editCommand = new EditCommand(\r
+ MessageManager.getString("action.edit_group"));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ message.append(MessageManager.getString("label.edit_sequence"))\r
+ .append(" " + seq.getName());\r
+ String label = seq.getName();\r
+ if (label.length() > 10)\r
+ {\r
+ label = label.substring(0, 10);\r
+ }\r
+ if (editCommand == null)\r
+ {\r
+ editCommand = new EditCommand(MessageManager.formatMessage(\r
+ "label.edit_params", new String[]\r
+ { label }));\r
+ }\r
+ }\r
+\r
+ if (insertGap)\r
+ {\r
+ message.append(" insert ");\r
+ }\r
+ else\r
+ {\r
+ message.append(" delete ");\r
+ }\r
+\r
+ message.append(Math.abs(startres - lastres) + " gaps.");\r
+ ap.alignFrame.statusBar.setText(message.toString());\r
+\r
+ // Are we editing within a selection group?\r
+ if (groupEditing\r
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())\r
+ .contains(seq)))\r
+ {\r
+ fixedColumns = true;\r
+\r
+ // sg might be null as the user may only see 1 sequence,\r
+ // but the sequence represents a group\r
+ if (sg == null)\r
+ {\r
+ if (!av.isHiddenRepSequence(seq))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ sg = av.getRepresentedSequences(seq);\r
+ }\r
+\r
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
+\r
+ if ((startres < fixedLeft && lastres >= fixedLeft)\r
+ || (startres >= fixedLeft && lastres < fixedLeft)\r
+ || (startres > fixedRight && lastres <= fixedRight)\r
+ || (startres <= fixedRight && lastres > fixedRight))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (fixedLeft > startres)\r
+ {\r
+ fixedRight = fixedLeft - 1;\r
+ fixedLeft = 0;\r
+ }\r
+ else if (fixedRight < startres)\r
+ {\r
+ fixedLeft = fixedRight;\r
+ fixedRight = -1;\r
+ }\r
+ }\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ fixedColumns = true;\r
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
+\r
+ if ((insertGap && startres > y1 && lastres < y1)\r
+ || (!insertGap && startres < y2 && lastres > y2))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ // Selection spans a hidden region\r
+ if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))\r
+ {\r
+ if (startres >= y2)\r
+ {\r
+ fixedLeft = y2;\r
+ }\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (groupEditing)\r
+ {\r
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())\r
+ .toArray(new SequenceI[0]);\r
+\r
+ // drag to right\r
+ if (insertGap)\r
+ {\r
+ // If the user has selected the whole sequence, and is dragging to\r
+ // the right, we can still extend the alignment and selectionGroup\r
+ if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight\r
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)\r
+ {\r
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);\r
+ fixedRight = sg.getEndRes();\r
+ }\r
+\r
+ // Is it valid with fixed columns??\r
+ // Find the next gap before the end\r
+ // of the visible region boundary\r
+ boolean blank = false;\r
+ for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)\r
+ {\r
+ blank = true;\r
+\r
+ for (SequenceI gs : groupSeqs)\r
+ {\r
+ for (int j = 0; j < startres - lastres; j++)\r
+ {\r
+ if (!Comparison.isGap(gs.getCharAt(fixedRight\r
+ - j)))\r
+ {\r
+ blank = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (blank)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!blank)\r
+ {\r
+ if (sg.getSize() == av.getAlignment().getHeight())\r
+ {\r
+ if ((av.hasHiddenColumns() && startres < av\r
+ .getColumnSelection().getHiddenBoundaryRight(startres)))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ int alWidth = av.getAlignment().getWidth();\r
+ if (av.hasHiddenRows())\r
+ {\r
+ int hwidth = av.getAlignment().getHiddenSequences()\r
+ .getWidth();\r
+ if (hwidth > alWidth)\r
+ {\r
+ alWidth = hwidth;\r
+ }\r
+ }\r
+ // We can still insert gaps if the selectionGroup\r
+ // contains all the sequences\r
+ sg.setEndRes(sg.getEndRes() + startres - lastres);\r
+ fixedRight = alWidth + startres - lastres;\r
+ }\r
+ else\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+\r
+ // drag to left\r
+ else if (!insertGap)\r
+ {\r
+ // / Are we able to delete?\r
+ // ie are all columns blank?\r
+\r
+ for (SequenceI gs : groupSeqs)\r
+ {\r
+ for (int j = startres; j < lastres; j++)\r
+ {\r
+ if (gs.getLength() <= j)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!Comparison.isGap(gs.getCharAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ insertChar(j, groupSeqs, fixedRight);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,\r
+ startres - lastres, av.getAlignment(), true);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ deleteChar(startres, groupSeqs, fixedRight);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,\r
+ lastres - startres, av.getAlignment(), true);\r
+ }\r
+\r
+ }\r
+ }\r
+ else\r
+ // ///Editing a single sequence///////////\r
+ {\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ insertChar(j, new SequenceI[]\r
+ { seq }, fixedRight);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]\r
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (!Comparison.isGap(seq.getCharAt(startres)))\r
+ {\r
+ endEditing();\r
+ break;\r
+ }\r
+ deleteChar(startres, new SequenceI[]\r
+ { seq }, fixedRight);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // could be a keyboard edit trying to delete none gaps\r
+ int max = 0;\r
+ for (int m = startres; m < lastres; m++)\r
+ {\r
+ if (!Comparison.isGap(seq.getCharAt(m)))\r
+ {\r
+ break;\r
+ }\r
+ max++;\r
+ }\r
+\r
+ if (max > 0)\r
+ {\r
+ editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]\r
+ { seq }, startres, max, av.getAlignment(), true);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ lastres = startres;\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ void insertChar(int j, SequenceI[] seq, int fixedColumn)\r
+ {\r
+ int blankColumn = fixedColumn;\r
+ for (int s = 0; s < seq.length; s++)\r
+ {\r
+ // Find the next gap before the end of the visible region boundary\r
+ // If lastCol > j, theres a boundary after the gap insertion\r
+\r
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
+ {\r
+ if (Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
+ {\r
+ // Theres a space, so break and insert the gap\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (blankColumn <= j)\r
+ {\r
+ blankColumn = fixedColumn;\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+\r
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,\r
+ av.getAlignment(), true);\r
+\r
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),\r
+ true);\r
+\r
+ }\r
+\r
+ void deleteChar(int j, SequenceI[] seq, int fixedColumn)\r
+ {\r
+\r
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),\r
+ true);\r
+\r
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,\r
+ av.getAlignment(), true);\r
+ }\r
+\r
+ // ////////////////////////////////////////\r
+ // ///Everything below this is for defining the boundary of the rubberband\r
+ // ////////////////////////////////////////\r
+ public void doMousePressedDefineMode(MouseEvent evt)\r
+ {\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
+ oldSeq = seq;\r
+ startWrapBlock = wrappedBlock;\r
+\r
+ if (seq == -1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+\r
+ if (sequence == null || res > sequence.getLength())\r
+ {\r
+ return;\r
+ }\r
+\r
+ stretchGroup = av.getSelectionGroup();\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.getAlignment().findGroup(sequence);\r
+ if (stretchGroup != null && res > stretchGroup.getStartRes()\r
+ && res < stretchGroup.getEndRes())\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
+\r
+ else if (!stretchGroup.getSequences(null).contains(sequence)\r
+ || stretchGroup.getStartRes() > res\r
+ || stretchGroup.getEndRes() < res)\r
+ {\r
+ stretchGroup = null;\r
+\r
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);\r
+\r
+ if (allGroups != null)\r
+ {\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if (allGroups[i].getStartRes() <= res\r
+ && allGroups[i].getEndRes() >= res)\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+\r
+ // DETECT RIGHT MOUSE BUTTON IN AWT\r
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)\r
+ {\r
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,\r
+ sequence.findPosition(res));\r
+\r
+ Vector<String> links = null;\r
+ if (allFeatures != null)\r
+ {\r
+ for (int i = 0; i < allFeatures.length; i++)\r
+ {\r
+ if (allFeatures[i].links != null)\r
+ {\r
+ if (links == null)\r
+ {\r
+ links = new Vector<String>();\r
+ }\r
+ for (int j = 0; j < allFeatures[i].links.size(); j++)\r
+ {\r
+ links.addElement(allFeatures[i].links.elementAt(j));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ APopupMenu popup = new APopupMenu(ap, null, links);\r
+ this.add(popup);\r
+ popup.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+\r
+ if (av.cursorMode)\r
+ {\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
+ }\r
+\r
+ // Only if left mouse button do we want to change group sizes\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ stretchGroup = sg;\r
+\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ public void doMouseReleasedDefineMode(MouseEvent evt)\r
+ {\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ stretchGroup.recalcConservation(); // always do this - annotation has own\r
+ // state\r
+ if (stretchGroup.cs != null)\r
+ {\r
+ stretchGroup.cs.alignmentChanged(stretchGroup,\r
+ av.getHiddenRepSequences());\r
+\r
+ if (stretchGroup.cs.conservationApplied())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ }\r
+ else\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ }\r
+ }\r
+ changeEndRes = false;\r
+ changeStartRes = false;\r
+ stretchGroup = null;\r
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());\r
+ ap.paintAlignment(true);\r
+ av.sendSelection();\r
+ }\r
+\r
+ public void doMouseDraggedDefineMode(MouseEvent evt)\r
+ {\r
+ int res = findRes(evt);\r
+ int y = findSeq(evt);\r
+\r
+ if (wrappedBlock != startWrapBlock)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ mouseDragging = true;\r
+\r
+ if (y > av.getAlignment().getHeight())\r
+ {\r
+ y = av.getAlignment().getHeight() - 1;\r
+ }\r
+\r
+ if (res >= av.getAlignment().getWidth())\r
+ {\r
+ res = av.getAlignment().getWidth() - 1;\r
+ }\r
+\r
+ if (stretchGroup.getEndRes() == res)\r
+ {\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
+ }\r
+ else if (stretchGroup.getStartRes() == res)\r
+ {\r
+ // Edit start res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
+\r
+ if (changeEndRes)\r
+ {\r
+ if (res > (stretchGroup.getStartRes() - 1))\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
+ }\r
+ else if (changeStartRes)\r
+ {\r
+ if (res < (stretchGroup.getEndRes() + 1))\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
+ }\r
+\r
+ int dragDirection = 0;\r
+\r
+ if (y > oldSeq)\r
+ {\r
+ dragDirection = 1;\r
+ }\r
+ else if (y < oldSeq)\r
+ {\r
+ dragDirection = -1;\r
+ }\r
+\r
+ while ((y != oldSeq) && (oldSeq > -1)\r
+ && (y < av.getAlignment().getHeight()))\r
+ {\r
+ // This routine ensures we don't skip any sequences, as the\r
+ // selection is quite slow.\r
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ oldSeq += dragDirection;\r
+\r
+ if (oldSeq < 0)\r
+ {\r
+ break;\r
+ }\r
+\r
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ if (stretchGroup.getSequences(null).contains(nextSeq))\r
+ {\r
+ stretchGroup.deleteSequence(seq, false);\r
+ }\r
+ else\r
+ {\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq, false);\r
+ }\r
+\r
+ stretchGroup.addSequence(nextSeq, false);\r
+ }\r
+ }\r
+\r
+ if (oldSeq < 0)\r
+ {\r
+ oldSeq = -1;\r
+ }\r
+\r
+ if (res > av.endRes || res < av.startRes || y < av.startSeq\r
+ || y > av.endSeq)\r
+ {\r
+ mouseExited(evt);\r
+ }\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ if (oldSeq < 0)\r
+ {\r
+ oldSeq = 0;\r
+ }\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ }\r
+\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (mouseDragging && scrollThread == null)\r
+ {\r
+ scrollThread = new ScrollThread();\r
+ }\r
+ }\r
+\r
+ void scrollCanvas(MouseEvent evt)\r
+ {\r
+ if (evt == null)\r
+ {\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ mouseDragging = false;\r
+ }\r
+ else\r
+ {\r
+ if (scrollThread == null)\r
+ {\r
+ scrollThread = new ScrollThread();\r
+ }\r
+\r
+ mouseDragging = true;\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ }\r
+\r
+ // this class allows scrolling off the bottom of the visible alignment\r
+ class ScrollThread extends Thread\r
+ {\r
+ MouseEvent evt;\r
+\r
+ boolean running = false;\r
+\r
+ public ScrollThread()\r
+ {\r
+ start();\r
+ }\r
+\r
+ public void setEvent(MouseEvent e)\r
+ {\r
+ evt = e;\r
+ }\r
+\r
+ public void stopScrolling()\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ running = true;\r
+ while (running)\r
+ {\r
+\r
+ if (evt != null)\r
+ {\r
+\r
+ if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ {\r
+ running = ap.scrollUp(true);\r
+ }\r
+\r
+ if (mouseDragging && evt.getY() >= getSize().height\r
+ && av.getAlignment().getHeight() > av.getEndSeq())\r
+ {\r
+ running = ap.scrollUp(false);\r
+ }\r
+\r
+ if (mouseDragging && evt.getX() < 0)\r
+ {\r
+ running = ap.scrollRight(false);\r
+ }\r
+\r
+ else if (mouseDragging && evt.getX() >= getSize().width)\r
+ {\r
+ running = ap.scrollRight(true);\r
+ }\r
+ }\r
+\r
+ try\r
+ {\r
+ Thread.sleep(75);\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * modify current selection according to a received message.\r
+ */\r
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,\r
+ SelectionSource source)\r
+ {\r
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel\r
+ // handles selection messages...\r
+ // TODO: extend config options to allow user to control if selections may be\r
+ // shared between viewports.\r
+ if (av != null\r
+ && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)\r
+ .getSequenceSetId().equals(av.getSequenceSetId()))))\r
+ {\r
+ return;\r
+ }\r
+\r
+ /*\r
+ * Check for selection in a view of which this one is a dna/protein\r
+ * complement.\r
+ */\r
+ if (selectionFromTranslation(seqsel, colsel, source))\r
+ {\r
+ return;\r
+ }\r
+\r
+ // do we want to thread this ? (contention with seqsel and colsel locks, I\r
+ // suspect)\r
+ // rules are: colsel is copied if there is a real intersection between\r
+ // sequence selection\r
+ boolean repaint = false, copycolsel = true;\r
+ if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))\r
+ {\r
+ SequenceGroup sgroup = null;\r
+ if (seqsel != null && seqsel.getSize() > 0)\r
+ {\r
+ if (av.getAlignment() == null)\r
+ {\r
+ System.out\r
+ .println("Selection message: alignviewport av SeqSetId="\r
+ + av.getSequenceSetId() + " ViewId="\r
+ + av.getViewId()\r
+ + " 's alignment is NULL! returning immediatly.");\r
+ return;\r
+ }\r
+ sgroup = seqsel.intersect(av.getAlignment(),\r
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);\r
+ if ((sgroup == null || sgroup.getSize() == 0)\r
+ && (colsel == null || colsel.size() == 0))\r
+ {\r
+ // don't copy columns if the region didn't intersect.\r
+ copycolsel = false;\r
+ }\r
+ }\r
+ if (sgroup != null && sgroup.getSize() > 0)\r
+ {\r
+ av.setSelectionGroup(sgroup);\r
+ }\r
+ else\r
+ {\r
+ av.setSelectionGroup(null);\r
+ }\r
+ repaint = av.isSelectionGroupChanged(true);\r
+ }\r
+ if (copycolsel\r
+ && (av.getColumnSelection() == null || !av\r
+ .isColSelChanged(true)))\r
+ {\r
+ // the current selection is unset or from a previous message\r
+ // so import the new colsel.\r
+ if (colsel == null || colsel.size() == 0)\r
+ {\r
+ if (av.getColumnSelection() != null)\r
+ {\r
+ av.getColumnSelection().clear();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // TODO: shift colSel according to the intersecting sequences\r
+ if (av.getColumnSelection() == null)\r
+ {\r
+ av.setColumnSelection(new ColumnSelection(colsel));\r
+ }\r
+ else\r
+ {\r
+ av.getColumnSelection().setElementsFrom(colsel);\r
+ }\r
+ }\r
+ repaint |= av.isColSelChanged(true);\r
+ }\r
+ if (copycolsel\r
+ && av.hasHiddenColumns()\r
+ && (av.getColumnSelection() == null || av.getColumnSelection()\r
+ .getHiddenColumns() == null))\r
+ {\r
+ System.err.println("Bad things");\r
+ }\r
+ if (repaint)\r
+ {\r
+ ap.scalePanelHolder.repaint();\r
+ ap.repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * scroll to the given row/column - or nearest visible location\r
+ * \r
+ * @param row\r
+ * @param column\r
+ */\r
+ public void scrollTo(int row, int column)\r
+ {\r
+\r
+ row = row < 0 ? ap.av.startSeq : row;\r
+ column = column < 0 ? ap.av.startRes : column;\r
+ ap.scrollTo(column, column, row, true, true);\r
+ }\r
+\r
+ /**\r
+ * scroll to the given row - or nearest visible location\r
+ * \r
+ * @param row\r
+ */\r
+ public void scrollToRow(int row)\r
+ {\r
+\r
+ row = row < 0 ? ap.av.startSeq : row;\r
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);\r
+ }\r
+\r
+ /**\r
+ * scroll to the given column - or nearest visible location\r
+ * \r
+ * @param column\r
+ */\r
+ public void scrollToColumn(int column)\r
+ {\r
+\r
+ column = column < 0 ? ap.av.startRes : column;\r
+ ap.scrollTo(column, column, ap.av.startSeq, true, true);\r
+ }\r
+\r
+ /**\r
+ * If this panel is a cdna/protein translation view of the selection source,\r
+ * tries to map the source selection to a local one, and returns true. Else\r
+ * returns false.\r
+ * \r
+ * @param seqsel\r
+ * @param colsel\r
+ * @param source\r
+ */\r
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,\r
+ ColumnSelection colsel, SelectionSource source)\r
+ {\r
+ if (!(source instanceof AlignViewportI)) {\r
+ return false;\r
+ }\r
+ final AlignViewportI sourceAv = (AlignViewportI) source;\r
+ if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)\r
+ {\r
+ return false;\r
+ }\r
+ \r
+ /*\r
+ * Map sequence selection\r
+ */\r
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);\r
+ av.setSelectionGroup(sg);\r
+ av.isSelectionGroupChanged(true);\r
+ \r
+ /*\r
+ * Map column selection\r
+ */\r
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,\r
+ av);\r
+ av.setColumnSelection(cs);\r
+ av.isColSelChanged(true);\r
+ \r
+ ap.scalePanelHolder.repaint();\r
+ ap.repaint();\r
+ \r
+ return true;\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff