From 788db94ce76b7bf2d76e979f30a8e61c68af75f4 Mon Sep 17 00:00:00 2001 From: jprocter Date: Sun, 17 Jun 2007 12:51:27 +0000 Subject: [PATCH] mouseOver highlighting and broadcasting efficiency --- src/jalview/gui/SeqPanel.java | 3575 +++++++++++++++++++++-------------------- 1 file changed, 1793 insertions(+), 1782 deletions(-) diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 37262bb..dc326de 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,1782 +1,1793 @@ -/* - * 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(SearchResults results) - { - seqCanvas.highlightSearchResults(results); - } - - 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 + * 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)) + { + // System.err.println("mouseOver Sequence: "+tmp); + ssm.mouseOverSequence(sequence, index); + } + lastMessage = tmp; + } + + + public void highlightSequence(SearchResults results) + { + seqCanvas.highlightSearchResults(results); + } + + 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); + int pos; + if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + { + return; + } + + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + + if (res >= sequence.getLength()) + { + return; + } + + pos = setStatusMessage(sequence, res, seq); + if (ssm != null && pos>-1) + mouseOverSequence(sequence, pos); + + + 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; + + /** + * 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 + */ + int setStatusMessage(SequenceI sequence, int res, int seq) + { + int pos=-1; + 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) + { + pos=sequence.findPosition(res); + if (obj != "") + { + text.append(obj + " (" + pos + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); + return pos; + } + + /** + * 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) + { + } + } + } + } +} -- 1.7.10.2