X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=e922a0d32666cf6d7df120d5532d975396f05cdf;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4ea3a12b062e6c6e46ceab9c36009791782bb601;hpb=7e1e1f7d676e4fdfb5ed61cb12319b46659d9290;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index 4ea3a12..e922a0d --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,1646 +1,2067 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 jalview.datamodel.*; -import jalview.commands.EditCommand; -import jalview.schemes.*; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; -import java.util.Vector; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener - -{ - /** 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; - - /** - * Creates a new SeqPanel object. - * - * @param avp DOCUMENT ME! - * @param p DOCUMENT ME! - */ - public SeqPanel(AlignViewport avp, AlignmentPanel p) - { - linkImageURL = getClass().getResource("/images/link.gif"); - ToolTipManager.sharedInstance().registerComponent(this); - ToolTipManager.sharedInstance().setInitialDelay(0); - ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = avp; - setBackground(Color.white); - - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas, BorderLayout.CENTER); - - ap = p; - - if (!av.isDataset()) - { - addMouseMotionListener(this); - addMouseListener(this); - addMouseWheelListener(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].getBegin() <= res) && - (features[i].getEnd() >= res)) - { - tmp.addElement(features[i]); - } - } - } - - features = new SequenceFeature[tmp.size()]; - for(int i=0; i= res) - { - if (av.featuresDisplayed.containsKey(sf.getType())) - { - allFeatures.addElement(sf); - } - } - index++; - } - } - return allFeatures; - } - - 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 = getKeyboardNo(keyboardNo1)-1; - scrollToVisible(); - } - - void setCursorColumn() - { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; - scrollToVisible(); - } - - void setCursorRowAndColumn() - { - if(keyboardNo2==null) - { - keyboardNo2 = new StringBuffer(); - } - else - { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; - seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; - scrollToVisible(); - } - } - - void setCursorPosition() - { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); - - seqCanvas.cursorX = sequence.findIndex( - getKeyboardNo(keyboardNo1)-1 - ); - scrollToVisible(); - } - - void moveCursor(int dx, int dy) - { - seqCanvas.cursorX += dx; - seqCanvas.cursorY += dy; - 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.startRes) - { - if (!ap.scrollRight(false)) - break; - } - while (seqCanvas.cursorX > 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 max) - max = index; - if(index < min) - min = index; - } - - max ++; - - if(topLeft) - { - sg.setStartRes(seqCanvas.cursorX); - if(sg.getEndRes()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(false).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.repaint(); - } - - void insertGapAtCursor(boolean group) - { - groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; - editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); - endEditing(); - } - - void deleteGapAtCursor(boolean group) - { - groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); - 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 getKeyboardNo(StringBuffer kb) - { - if(kb==null) - return 1; - else - return Integer.parseInt(kb.toString()); - } - - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) - { - mouseDragging = false; - mouseWheelPressed = false; - - if (!editingSeqs) - { - doMouseReleasedDefineMode(evt); - return; - } - - endEditing(); - - ap.repaint(); - } - - - - /** - * 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; - } - - /** - * 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(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) - { - seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); - } - - setStatusMessage(sequence, res, seq); - - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) - { - tooltipText.setLength(6); // Cuts the buffer back to - - 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(" "); - - } - - // else if(features[i].begin==0 && features[i].end==0) - { - // seqSpecific.append(features[i].featureGroup+": " - // + features[i].getType()+" " - // +features[i].getDescription()+"
"); - - } - } - - if(tooltipText.length()==6) // - { - - setToolTipText(""); - } - else - { - tooltipText.append(""); - setToolTipText(tooltipText.toString()); - } - } - else - setToolTipText(""); - } - } - - 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.repaint(); - } - - 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(); - - - if (!groupEditing && av.hasHiddenRows) - { - if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) - { - groupEditing = true; - } - } - - //No group, but the sequence may represent a group - if (groupEditing - && sg == null - && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) - { - groupEditing = false; - } - - SequenceI seq = av.alignment.getSequenceAt(startseq); - 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(true).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) - { - sg = new SequenceGroup(null, null, false, false, false, 0, - av.alignment.getWidth()-1); - sg.addSequence(av.alignment.getSequenceAt(startseq), false); - } - - 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(fixedLefty2 || fixedRight==-1)) - { - if(startres>=y2) - { - fixedLeft = y2; - } - else - { - fixedRight = y2 - 1; - } - } - } - - - if (groupEditing) - { - Vector vseqs = sg.getSequences(true); - 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(false) == av.alignment.getHeight() ) - { - if((av.hasHiddenColumns - && startresalWidth) - 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.getGapCharacter(), - 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.getGapCharacter(), - 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.getGapCharacter(), - 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; m0) - { - editCommand.appendEdit(EditCommand.DELETE_GAP, - new SequenceI[] - {seq}, - startres, max, - av.getGapCharacter(), - true); - } - } - } - } - - lastres = startres; - seqCanvas.repaint(); - } - - - - void insertChar(int j, SequenceI [] seq, int fixedColumn) - { - int blankColumn = fixedColumn; - for(int s=0; s 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.getGapCharacter(), true); - - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - j, 1, av.getGapCharacter(), - true); - - } - - void deleteChar(int j, SequenceI [] seq, int fixedColumn) - { - - editCommand.appendEdit(EditCommand.DELETE_GAP, - seq, - j, 1, av.getGapCharacter(), true); - - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - fixedColumn, 1, av.getGapCharacter(), 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(false) == 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==1) - { - 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); - - seqCanvas.highlightSearchResults(null); - } - } - } - - public void mouseWheelMoved(MouseWheelEvent e) - { - e.consume(); - /* if (mouseWheelPressed) - { - Font font = av.getFont(); - int fontSize = font.getSize(); - if (e.getWheelRotation() > 0 && fontSize < 51) - fontSize++; - else if (fontSize > 1) - fontSize--; - - - - av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); - - ap.fontChanged(); - } - else*/ - { - 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(false).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)) - { - Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - Vector links = new Vector(); - for (int i = 0; i < allFeatures.size(); i++) - { - SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); - if (sf.links != null) - { - for (int j = 0; j < sf.links.size(); j++) - { - links.addElement(sf.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(true), - 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()); - } - } - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; - - PaintRefresher.Refresh(this, av.getSequenceSetId()); - } - - /** - * 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(false).contains(nextSeq)) - { - stretchGroup.deleteSequence(seq, false); - } - else - { - if (seq != null) - { - stretchGroup.addSequence(seq, false); - } - - stretchGroup.addSequence(nextSeq, false); - } - } - - if(oldSeq < 0) - oldSeq = -1; - - mouseDragging = true; - - if (scrollThread != null) - { - scrollThread.setEvent(evt); - } - - seqCanvas.repaint(); - } - - void scrollCanvas(MouseEvent evt) - { - if(evt==null) - { - if(scrollThread!=null) - { - scrollThread.running = false; - scrollThread = null; - } - mouseDragging = false; - } - else - { - if (scrollThread == null) - scrollThread = new ScrollThread(); - - mouseDragging = true; - scrollThread.setEvent(evt); - } - - } - - - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread extends Thread - { - MouseEvent evt; - boolean running = false; - - public ScrollThread() - { - start(); - } - - public void setEvent(MouseEvent e) - { - evt = e; - } - - public void stopScrolling() - { - running = false; - } - - public void run() - { - running = true; - - while (running) - { - if (evt != null) - { - if (mouseDragging && (evt.getY() < 0) && - (av.getStartSeq() > 0)) - { - running = ap.scrollUp(true); - } - - if (mouseDragging && (evt.getY() >= getHeight()) && - (av.alignment.getHeight() > av.getEndSeq())) - { - running = ap.scrollUp(false); - } - - if (mouseDragging && (evt.getX() < 0)) - { - running = ap.scrollRight(false); - } - else if (mouseDragging && (evt.getX() >= getWidth())) - { - running = ap.scrollRight(true); - } - } - - try - { - Thread.sleep(20); - } - catch (Exception ex) - { - } - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.api.AlignViewportI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentI; +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.io.SequenceAnnotationReport; +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.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.List; +import java.util.Vector; + +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.ToolTipManager; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.130 $ + */ +public class SeqPanel extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener, SequenceListener, + SelectionListener + +{ + /** 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; + + private final SequenceAnnotationReport seqARep; + + StringBuffer tooltipText = new StringBuffer(); + + String tmpString; + + EditCommand editCommand; + + StructureSelectionManager ssm; + + SearchResults lastSearchResults; + + /** + * 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"); + seqARep = new SequenceAnnotationReport(linkImageURL.toString()); + 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 = av.getStructureSelectionManager(); + ssm.addStructureViewerListener(this); + ssm.addSelectionListener(this); + } + } + + int startWrapBlock = -1; + + int wrappedBlock = -1; + + /** + * Returns the aligned sequence position (base 0) at the mouse position, or + * the closest visible one + * + * @param evt + * @return + */ + 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(this.getWidth()); + if (cwidth < 1) + { + return 0; + } + + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; + + res = wrappedBlock * cwidth + x / av.getCharWidth(); + + } + else + { + if (x > seqCanvas.getX() + seqCanvas.getWidth()) + { + // make sure we calculate relative to visible alignment, rather than + // right-hand gutter + x = seqCanvas.getX() + seqCanvas.getWidth(); + } + res = (x / av.getCharWidth()) + av.getStartRes(); + if (res > av.getEndRes()) + { + // moused off right + res = av.getEndRes(); + } + } + + if (av.hasHiddenColumns()) + { + res = av.getColumnSelection().adjustForHiddenColumns(res); + } + + return res; + + } + + int findSeq(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); + } + else + { + seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + .getAlignment().getHeight() - 1); + } + + return seq; + } + + /** + * When all of a sequence of edits are complete, put the resulting edit list + * on the history stack (undo list), and reset flags for editing in progress. + */ + void endEditing() + { + try + { + if (editCommand != null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, av.getAlignment() + .getSequences()); + } + } finally + { + /* + * Tidy up come what may... + */ + 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); + } + if (!av.getWrapAlignment()) + { + 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.getSequences(null).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, false, seqCanvas.cursorX + getKeyboardNo1()); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX + getKeyboardNo1(); + editSequence(false, false, seqCanvas.cursorX); + endEditing(); + } + + void insertNucAtCursor(boolean group, String nuc) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); + 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; + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } + + endEditing(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + 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; + + @Override + public void mouseOverSequence(SequenceI sequence, int index, int pos) + { + String tmp = sequence.hashCode() + " " + index + " " + pos; + + if (lastMessage == null || !lastMessage.equals(tmp)) + { + // System.err.println("mouseOver Sequence: "+tmp); + ssm.mouseOverSequence(sequence, index, pos, av); + } + lastMessage = tmp; + } + + /** + * Highlight the mapped region described by the search results object (unless + * unchanged). This supports highlight of protein while mousing over linked + * cDNA and vice versa. The status bar is also updated to show the location of + * the start of the highlighted region. + */ + @Override + public void highlightSequence(SearchResults results) + { + if (results == null || results.equals(lastSearchResults)) + { + return; + } + lastSearchResults = results; + + if (av.isFollowHighlight()) + { + /* + * if scrollToPosition requires a scroll adjustment, this flag prevents + * another scroll event being propagated back to the originator + * + * @see AlignmentPanel#adjustmentValueChanged + */ + ap.setFollowingComplementScroll(true); + if (ap.scrollToPosition(results, false)) + { + seqCanvas.revalidate(); + } + } + setStatusMessage(results); + seqCanvas.highlightSearchResults(results); + } + + @Override + public VamsasSource getVamsasSource() + { + return this.ap == null ? null : this.ap.av; + } + + @Override + public void updateColours(SequenceI seq, int index) + { + System.out.println("update the seqPanel colours"); + // repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + 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, res, pos); + } + + tooltipText.setLength(6); // Cuts the buffer back to + + 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()); + } + + if (groups[g].getDescription() != null) + { + tooltipText.append(": " + groups[g].getDescription()); + } + } + } + } + + // use aa to see if the mouse pointer is on a + if (av.isShowSequenceFeatures()) + { + int rpos; + List features = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + rpos = sequence.findPosition(res)); + seqARep.appendFeatures(tooltipText, rpos, features, + this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); + } + if (tooltipText.length() == 6) // + { + setToolTipText(null); + lastTooltip = null; + } + else + { + if (lastTooltip == null + || !lastTooltip.equals(tooltipText.toString())) + { + String formatedTooltipText = JvSwingUtils.wrapTooltip(true, + tooltipText.toString()); + // String formatedTooltipText = tooltipText.toString(); + setToolTipText(formatedTooltipText); + lastTooltip = tooltipText.toString(); + } + + } + + } + + private Point lastp = null; + + /* + * (non-Javadoc) + * + * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) + */ + public Point getToolTipLocation(MouseEvent event) + { + int x = event.getX(), w = getWidth(); + int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too + // close to edge + Point p = lastp; + if (!event.isShiftDown() || p == null) + { + p = (tooltipText != null && tooltipText.length() > 6) ? new Point( + event.getX() + wdth, event.getY() - 20) : null; + } + /* + * TODO: try to modify position region is not obcured by tooltip + */ + return lastp = p; + } + + 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) + { + StringBuilder text = new StringBuilder(32); + + /* + * Sequence number (if known), and sequence name. + */ + 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" : ("*" + .equals(displayChar) ? "STOP" : 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(")"); + } + ap.alignFrame.statusBar.setText(text.toString()); + return pos; + } + + /** + * Set the status bar message to highlight the first matched position in + * search results. + * + * @param results + */ + private void setStatusMessage(SearchResults results) + { + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return; + } + SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + for (Match m : results.getResults()) + { + SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + + if (seq == ds) + { + /* + * Convert position in sequence (base 1) to sequence character array + * index (base 0) + */ + int start = m.getStart() - 1; + setStatusMessage(seq, start, sequenceIndex); + return; + } + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + 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.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), + true); + av.setCharWidth(oldWidth); + ap.fontChanged(); + } + else + { + if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) + { + av.setCharWidth(av.getCharWidth() - 1); + } + else if (evt.getX() > lastMousePress.getX()) + { + av.setCharWidth(av.getCharWidth() + 1); + } + + ap.paintAlignment(false); + } + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); + + 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, false, res); + } + else + { + editSequence(true, false, res); + } + + mouseDragging = true; + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } + } + + // TODO: Make it more clever than many booleans + synchronized void editSequence(boolean insertGap, boolean editSeq, + int startres) + { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); + + SequenceI seq = av.getAlignment().getSequenceAt(startseq); + + // No group, but the sequence may represent a group + if (!groupEditing && av.hasHiddenRows()) + { + if (av.isHiddenRepSequence(seq)) + { + sg = av.getRepresentedSequences(seq); + groupEditing = true; + } + } + + StringBuilder message = new StringBuilder(64); + if (groupEditing) + { + message.append("Edit group:"); + if (editCommand == null) + { + editCommand = new EditCommand( + MessageManager.getString("action.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(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) + { + List vseqs = sg.getSequences(av.getHiddenRepSequences()); + int g, groupSize = vseqs.size(); + SequenceI[] groupSeqs = new SequenceI[groupSize]; + for (g = 0; g < groupSeqs.length; g++) + { + groupSeqs[g] = vseqs.get(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.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 (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.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 (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 + { + appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres + - lastres); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) + { + deleteChar(startres, groupSeqs, fixedRight); + } + } + else + { + appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres + - startres); + } + + } + } + 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 + { + appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, + startres - lastres); + } + } + else + { + if (!editSeq) + { + // 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) + { + appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, + startres, max); + } + } + } + else + {// insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] { seq }, fixedRight); + } + } + else + { + appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, + startres - lastres); + } + } + } + } + + 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; + } + } + + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); + + appendEdit(Action.INSERT_GAP, seq, j, 1); + + } + + /** + * Helper method to add and perform one edit action. + * + * @param action + * @param seq + * @param pos + * @param count + */ + protected void appendEdit(Action action, SequenceI[] seq, int pos, + int count) + { + + final Edit edit = new EditCommand().new Edit(action, seq, pos, count, + av.getAlignment().getGapCharacter()); + + editCommand.appendEdit(edit, av.getAlignment(), true, null); + } + + void deleteChar(int j, SequenceI[] seq, int fixedColumn) + { + + appendEdit(Action.DELETE_GAP, seq, j, 1); + + appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + { + oldSeq = 0; + } + + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; + } + + if (mouseDragging) + { + scrollThread = new ScrollThread(); + } + } + + @Override + public void mouseClicked(MouseEvent evt) + { + SequenceGroup sg = null; + SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); + if (evt.getClickCount() > 1) + { + sg = av.getSelectionGroup(); + if (sg != null && sg.getSize() == 1 + && sg.getEndRes() - sg.getStartRes() < 2) + { + av.setSelectionGroup(null); + } + + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt))); + + if (features != null && features.size() > 0) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); + seqCanvas.highlightSearchResults(highlight); + } + if (features != null && features.size() > 0) + { + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] { sequence }, + features.toArray(new SequenceFeature[features.size()]), + false, ap); + + seqCanvas.highlightSearchResults(null); + } + } + } + + @Override + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + if (e.getWheelRotation() > 0) + { + if (e.isShiftDown()) + { + ap.scrollRight(true); + + } + else + { + ap.scrollUp(false); + } + } + else + { + if (e.isShiftDown()) + { + ap.scrollRight(false); + } + else + { + ap.scrollUp(true); + } + } + // TODO Update tooltip for new position. + } + + /** + * 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.getWrapAlignment() && seq > av.getAlignment().getHeight()) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.cannot_edit_annotations_in_wrapped_view"), + MessageManager.getString("label.wrapped_view_no_edit"), + JOptionPane.WARNING_MESSAGE); + return; + } + + if (seq < 0 || res < 0) + { + 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); + + } + + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + { + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector(); + for (SequenceFeature sf : allFeatures) + { + if (sf.links != null) + { + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.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; + } + + 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()); + } + } + PaintRefresher.Refresh(this, av.getSequenceSetId()); + ap.paintAlignment(true); + + changeEndRes = false; + changeStartRes = false; + stretchGroup = null; + av.sendSelection(); + } + + /** + * 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.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 < 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.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; + } + + 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; + } + + @Override + 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.getAlignment().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) + { + } + } + } + } + + /** + * modify current selection according to a received message. + */ + @Override + 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. + boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) + .getSequenceSetId().equals(av.getSequenceSetId()))); + if (iSentTheSelection || !av.followSelection) + { + return; + } + + /* + * Ignore the selection if there is one of our own pending. + */ + if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + { + 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; + boolean copycolsel = true; + + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize() > 0) + { + if (av.getAlignment() == null) + { + jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediately."); + 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); + } + av.isSelectionGroupChanged(true); + repaint = true; + + if (copycolsel) + { + // 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(); + repaint = true; + } + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.getColumnSelection() == null) + { + av.setColumnSelection(new ColumnSelection(colsel)); + } + else + { + av.getColumnSelection().setElementsFrom(colsel); + } + } + av.isColSelChanged(true); + repaint = true; + } + + if (copycolsel + && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection() + .getHiddenColumns() == null)) + { + System.err.println("Bad things"); + } + if (repaint) // always true! + { + // probably finessing with multiple redraws here + PaintRefresher.Refresh(this, av.getSequenceSetId()); + // ap.paintAlignment(false); + } + } + + /** + * 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); + + PaintRefresher.Refresh(this, av.getSequenceSetId()); + + return true; + } +}