X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=bc8f20009598607f32aa1905ab161c11183284b6;hb=519ea38fa40b0d2e7b3979268f19415f14e1e888;hp=ebcbc76d50f9f185a059fe1828a622180d027626;hpb=a11e13d8fffacf8115a4d83e4254bf94a87d6600;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index ebcbc76..bc8f200 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,492 +1,1017 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 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.analysis.*; + +import jalview.datamodel.*; + +import jalview.schemes.*; + import java.awt.*; import java.awt.event.*; -import jalview.datamodel.*; + +import java.util.*; + import javax.swing.*; -import jalview.schemes.*; -import jalview.analysis.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class SeqPanel extends JPanel { + /** DOCUMENT ME!! */ + public SeqCanvas seqCanvas; + + /** DOCUMENT ME!! */ + public AlignmentPanel ap; + protected int lastres; + protected int startseq; + int startEdit = -1; + int endEdit = -1; + protected AlignViewport av; + + // if character is inserted or deleted, we will need to recalculate the conservation + int seqEditOccurred = -1; + 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; + + boolean mouseWheelPressed = false; + + /** + * Creates a new SeqPanel object. + * + * @param avp DOCUMENT ME! + * @param p DOCUMENT ME! + */ + public SeqPanel(AlignViewport avp, AlignmentPanel p) + { + ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().setInitialDelay(0); + ToolTipManager.sharedInstance().setDismissDelay(10000); + this.av = avp; + setBackground(Color.white); - public SeqCanvas seqCanvas; - public AlignmentPanel parent; + seqCanvas = new SeqCanvas(avp); + setLayout(new BorderLayout()); + add(seqCanvas, BorderLayout.CENTER); - protected int startres; - protected int lastres; - protected int endres; + ap = p; - protected int startseq; - protected int padseq; + addMouseMotionListener(new MouseMotionAdapter() + { + public void mouseMoved(MouseEvent evt) + { + if (av.getWrapAlignment()) + { + return; + } - public boolean editFlag; - protected AlignViewport av; + doMouseMoved(evt); + } - // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; + public void mouseDragged(MouseEvent evt) + { + if (av.getWrapAlignment()) + { + return; + } + + if (editingSeqs) + { + doMouseDragged(evt); + } + else + { + doMouseDraggedDefineMode(evt); + } + } + }); + + addMouseWheelListener(new MouseWheelListener() + { + public void mouseWheelMoved(MouseWheelEvent e) + { - public SeqPanel(AlignViewport avp, AlignmentPanel p) { - this.av = avp; + if (mouseWheelPressed) + { + Font font = av.getFont(); + int fontSize = font.getSize(); + if (e.getWheelRotation() > 0 && fontSize < 30) + 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); + } - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas, BorderLayout.CENTER); + } + }); - parent = p; - addMouseMotionListener( new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { doMouseMoved(evt); } - public void mouseDragged(MouseEvent evt) - { - if(av.groupDefiningMode) - doMouseDraggedDefineMode(evt); - else - doMouseDragged(evt); - } - }); + addMouseListener(new MouseAdapter() + { + public void mouseReleased(MouseEvent evt) + { + mouseWheelPressed = false; + if (av.getWrapAlignment()) + { + return; + } + + if (editingSeqs) + { + doMouseReleased(evt); + } + else + { + doMouseReleasedDefineMode(evt); + } + } + + public void mousePressed(MouseEvent evt) + { + if( javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + return; + } + if (av.getWrapAlignment()) + { + return; + } + + if (evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + { + if (evt.isAltDown() || evt.isControlDown()) + { + groupEditing = true; + } + + editingSeqs = true; + doMousePressed(evt); + } + else + { + doMousePressedDefineMode(evt); + } + } + + public void mouseExited(MouseEvent evt) + { + if (av.getWrapAlignment() || editingSeqs) + { + return; + } + + doMouseExitedDefineMode(evt); + } + + public void mouseEntered(MouseEvent evt) + { + if (av.getWrapAlignment() || editingSeqs) + { + return; + } + + doMouseEnteredDefineMode(evt); + } + }); + } - addMouseListener( new MouseAdapter() + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleased(MouseEvent evt) { - public void mouseReleased(MouseEvent evt) - { - if(av.groupDefiningMode) - doMouseReleasedDefineMode(evt); - else - doMouseReleased(evt); - } - public void mousePressed(MouseEvent evt) - { - if(av.groupDefiningMode) - doMousePressedDefineMode(evt); - else - doMousePressed(evt); - } + if (seqEditOccurred > -1) + { + editOccurred(seqEditOccurred); + } - }); - repaint(); - } + startseq = -1; + lastres = -1; + seqEditOccurred = -1; + editingSeqs = false; + groupEditing = false; + ap.repaint(); + } - public void doMouseReleased(MouseEvent evt) { + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressed(MouseEvent evt) + { + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); - int x = evt.getX(); - int res = x/av.getCharWidth() + av.getStartRes(); + int seq; + int res; - endres = res; + int x = evt.getX(); + int y = evt.getY(); - // This is to detect edits - we're at the end of an edit if mouse is up - editFlag = false; - startseq = -1; - startres = -1; - lastres = -1; - if(seqEditOccurred>-1) - updateConservation(seqEditOccurred); + res = (x / av.getCharWidth()) + av.getStartRes(); + seq = (y / av.getCharHeight()) + av.getStartSeq(); - seqEditOccurred = -1; + if ((seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } - parent.RefreshPanels(); - repaint(); + startEdit = lastres; + endEdit = lastres; - } + return; + } - public void doMousePressed(MouseEvent evt) { - parent.alignFrame.addHistoryItem("sequence edit"); - int seq; - int res; + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseMoved(MouseEvent evt) + { + int res = 0; + int seq = 0; + int x = evt.getX(); + int y = evt.getY(); - int x = evt.getX(); - int y = evt.getY(); + if (av.wrapAlignment) + { + y -= (2 * av.charHeight); - res = x/av.getCharWidth() + av.getStartRes(); - seq = y/av.getCharHeight() + av.getStartSeq(); + int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; - if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength()) - { - //char resstr = align.getSequenceAt(seq).getSequence().charAt(res); - // Find the residue's position in the sequence (res is the position - // in the alignment + res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) + + (x / av.getCharWidth()) + av.getStartRes(); - startseq = seq; + y %= chunkHeight; + seq = (y / av.getCharHeight()) + av.getStartSeq(); + } + else + { + res = (x / av.getCharWidth()) + av.getStartRes(); + seq = (y / av.getCharHeight()) + av.getStartSeq(); + } - if (startseq == (av.getAlignment().getHeight()-1)) { - padseq = 1; - } else { - padseq = 1; - } + if (seq >= av.getAlignment().getHeight()) + { + return; + } - startres = res; - lastres = res; + SequenceI sequence = av.getAlignment().getSequenceAt(seq); - } else { - startseq = -1; - startres = -1; - lastres = -1; - } + if (res > sequence.getLength()) + { + return; + } - return; - } + Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + + ""); + String aa = ""; - public void doMouseMoved(MouseEvent evt) - { - int res=0, seq=0; - int x = evt.getX(); - int y = evt.getY(); - if(av.wrapAlignment) - { - y -= 2*av.charHeight; - int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight; + if (obj != null) + { + aa = obj.toString(); + } + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); - res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes(); + if (aa != "") + { + text.append(" Residue: " + aa + " (" + + av.getAlignment().getSequenceAt(seq).findPosition(res) + ")"); + } - System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) ); - y %= chunkHeight; - seq = y / av.getCharHeight() + av.getStartSeq(); + ap.alignFrame.statusBar.setText(text.toString()); - // chunkHeight = (da.getHeight() + 2)*charHeight; - // startx += chunkWidth; - } - else - { - res = x / av.getCharWidth() + av.getStartRes(); - seq = y / av.getCharHeight() + av.getStartSeq(); - } + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + Vector features = sequence.getSequenceFeatures(); + Enumeration e = features.elements(); + StringBuffer sbuffer = new StringBuffer(); + while (e.hasMoreElements()) + { + SequenceFeature sf = (SequenceFeature) e.nextElement(); - if(seq>=av.getAlignment().getHeight()) - return; + if ((sf.getStart() <= sequence.findPosition(res)) && + (sf.getEnd() >= sequence.findPosition(res))) + { + if (sbuffer.length() > 0) + { + sbuffer.append("; "); + } - Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ; - String aa = ""; - if(obj!=null) - aa = obj.toString(); + sbuffer.append(sf.getType() + " " + sf.getDescription()); - StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName()); - if(aa!="") - text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")"); + if (sf.getStatus().length() > 0) + { + sbuffer.append(" (" + sf.getStatus() + ")"); + } + } + } - parent.alignFrame.statusBar.setText(text.toString()); + this.setToolTipText(sbuffer.toString()); + } + } - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseDragged(MouseEvent evt) + { + // If we're dragging we're editing + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - public void doMouseDragged(MouseEvent evt) { - // If we're dragging we're editing - editFlag = true; - int x = evt.getX(); + if (res < 0) + { + res = 0; + } - int res = x/av.getCharWidth() + av.getStartRes(); - if (res < 0) {res = 0;} + if ((lastres == -1) || (lastres == res)) + { + return; + } - if (res != lastres) { - if (startseq != -1) { + boolean dragRight = true; - // Group editing - if (av.getGroupEdit()) { - SequenceGroup sg = av.getAlignment().findGroup(startseq); + if ((res < av.getAlignment().getWidth()) && (res < lastres)) + { + dragRight = false; + } - if(sg!=null) - if (res < av.getAlignment().getWidth() && res < lastres) - { - boolean flag = false; - for (int i= 0 ; i < sg.getSize(); i++) + if (res != lastres) + { + // Group editing + if (groupEditing) { - SequenceI s = (SequenceI)sg.getSequenceAt(i); - for (int j=lastres-1; j >= res; j--) - { - if (!flag) + SequenceGroup sg = av.getSelectionGroup(); + + if (sg == null) { - if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() && - s.getSequence().charAt(j)==' ') - { - res = j+1; - flag = true; - } - } - } - } - } - - if(sg!=null) - for (int i= 0 ; i < sg.getSize(); i++) - { - SequenceI s = (SequenceI)sg.getSequenceAt(i); - boolean found = false; - int sno = -1; - for (int k = 0; k < av.getAlignment().getHeight(); k++) + lastres = -1; + + return; + } + + // drag to right + if (dragRight) + { + sg.setEndRes(sg.getEndRes() + (res - lastres)); + } + + // drag to left + else + { + /// Are we able to delete? + // ie are all columns blank? + boolean deleteAllowed = false; + + for (int s = 0; s < sg.getSize(); s++) + { + SequenceI seq = sg.getSequenceAt(s); + + for (int j = res; j < lastres; j++) + { + if (seq.getSequence().length() <= j) + { + continue; + } + + if (!jalview.util.Comparison.isGap( + seq.getSequence().charAt(j))) + { + // Not a gap, block edit not valid + res = j + 1; + deleteAllowed = false; + + continue; + } + + deleteAllowed = true; + } + } + + if (!deleteAllowed) + { + lastres = -1; + + return; + } + + sg.setEndRes(sg.getEndRes() - (lastres - res)); + } + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI s = sg.getSequenceAt(i); + int k = av.alignment.findIndex(s); + + // drag to right + if (dragRight) + { + for (int j = lastres; j < res; j++) + { + insertChar(j, k); + } + } + + // drag to left + else + { + for (int j = res; j < lastres; j++) + { + if (s.getLength() > j) + { + deleteChar(res, k); + } + } + } + } + } + else /////Editing a single sequence/////////// { - if (av.getAlignment().getSequenceAt(k) == s) - { - found = true; - sno = k; - break; - } - } - if (found && sno != -1) { - if (res < av.getAlignment().getWidth() && res > lastres) - { - for (int j = lastres; j < res; j++) - insertChar(j,sno); - - int index = av.getAlignment().findIndex(s); - if (index != -1) - drawChars(index,index+1,lastres); - - - } else if (res < av.getAlignment().getWidth() && res < lastres) - { - for (int j = res; j < lastres; j++) + if ((res < av.getAlignment().getWidth()) && (res > lastres)) + { + // dragging to the right + for (int j = lastres; j < res; j++) + { + insertChar(j, startseq); + } + } + else if ((res < av.getAlignment().getWidth()) && + (res < lastres)) { - deleteChar(j,res,sno); - startres = res; - } - int index = av.getAlignment().findIndex(s); - if (index != -1) - drawChars(index,index+1,res); + // dragging to the left + for (int j = lastres; j > res; j--) + { + if (jalview.util.Comparison.isGap( + av.alignment.getSequenceAt(startseq) + .getSequence().charAt(res))) + { + deleteChar(res, startseq); + } + else + { + break; + } + } + } + } + } + + endEdit = res; + lastres = res; + seqCanvas.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param seqstart DOCUMENT ME! + * @param seqend DOCUMENT ME! + * @param start DOCUMENT ME! + */ + public void drawChars(int seqstart, int seqend, int start) + { + seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, + seqend, av.getStartRes(), av.getStartSeq(), 0); + seqCanvas.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + public void insertChar(int j, int seq) + { + av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = seq; + } + + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + public void deleteChar(int j, int seq) + { + av.alignment.getSequenceAt(seq).deleteCharAt(j); + seqEditOccurred = seq; - } - } + av.alignment.getWidth(); + seqCanvas.repaint(); + } - } - lastres = res; - } else { + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + */ + void editOccurred(int i) + { + if (endEdit == startEdit) + { + ap.alignFrame.historyList.pop(); + ap.alignFrame.updateEditMenuBar(); + } + av.updateConservation(); + av.updateConsensus(); - if (res < av.getAlignment().getWidth() && res > lastres) { - // dragging to the right - for (int j = lastres; j < res; j++) - insertChar(j,startseq); + //Does the edit affect any groups? + ////////////////////////////// + Vector groupsToUpdate = new Vector(); + SequenceGroup sg = av.getSelectionGroup(); - drawChars(startseq,startseq+1,lastres); + int s, g, gSize = av.alignment.getGroups().size(); + if (sg != null) + { + groupsToUpdate.addElement(av.getSelectionGroup()); + int sSize = sg.getSize(); + for (s = 0; s < sSize; s++) + { + SequenceI seq = sg.getSequenceAt(s); - } else if (res < av.getAlignment().getWidth() && res < lastres) + for (g = 0; g < gSize; g++) { + SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups(). + elementAt( + g); + if (sg2.sequences.contains(seq)) + { + if (!groupsToUpdate.contains(sg2)) + groupsToUpdate.addElement(sg2); + continue; + } + } + } + } + else + { + SequenceI seq = av.alignment.getSequenceAt(startseq); + for (g = 0; g < gSize; g++) + { + SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt( + g); + if (sg2.sequences.contains(seq)) + { + if (!groupsToUpdate.contains(sg2)) + groupsToUpdate.addElement(sg2); + continue; + } + } + } - // dragging to the left - for (int j = res; j < lastres; j++) { - deleteChar(j,res,startseq); - startres = res; - } - drawChars(startseq,startseq+1,res); - } - } + gSize = groupsToUpdate.size(); + for (g = 0; g < gSize; g++) + { + ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation(); } - lastres = res; + ////End of updating groups + ////////////////////////////////////////// + + // Y O Y CLUSTALX + ColourSchemeI cs = av.getGlobalColourScheme(); + if(cs!=null) + { + if (cs.conservationApplied()) + { + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + av.alignment.getSequences(), + 0, av.alignment.getWidth() - 1); + c.calculate(); + c.verdict(false, av.ConsPercGaps); + + if (cs instanceof ClustalxColourScheme) + { + ClustalxColourScheme cxs = (ClustalxColourScheme) cs; + cxs.resetClustalX(av.alignment.getSequences(), + av.alignment.getWidth()); + cs.setConservation(c); + av.setGlobalColourScheme(cs); + } + else + { + cs.setConservation(c); + av.setGlobalColourScheme(cs); + } + + } + + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(), + av.alignment.getWidth()); + av.setGlobalColourScheme(cs); + } + } } - repaint(); - return; - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressedDefineMode(MouseEvent evt) + { + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq(); + oldSeq = seq; - public void drawChars(int seqstart, int seqend, int start) { - seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0); - repaint(); - } + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - public void insertChar(int j, int seq) - { - av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred=seq; - } + if ((sequence == null) || (res > sequence.getLength())) + { + return; + } - public void deleteChar(int j, int res, int seq) - { + stretchGroup = av.getSelectionGroup(); - if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' || - av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' || - av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' ) - { - av.getAlignment().getSequenceAt(seq).deleteCharAt(j); - } + 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.sequences.contains(sequence) || + (stretchGroup.getStartRes() > res) || + (stretchGroup.getEndRes() < res)) + { + stretchGroup = null; - av.getAlignment().getWidth(); - repaint(); - seqEditOccurred=seq; - } + 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]; + av.setSelectionGroup(stretchGroup); + + break; + } + } + } + } - void updateConservation(int i) - { - Alignment al = (Alignment) av.getAlignment(); - SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i)); - if(sg==null || !(sg.cs instanceof ConservationColourScheme)) - return; + if (stretchGroup == null) + { + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), "Background"); + } + + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + } + else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + { + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); + pop.show(this, evt.getX(), evt.getY()); - Conservation c = sg.getConservation(); + // edit the properties of existing group + } - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth()); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - ccs.conserve = c; - } + 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(); - public void setColourScheme(ColourSchemeI cs, boolean showConservation) - { - seqCanvas.paintFlag = true; - if (av.getSelection().size() == 0) - { - seqCanvas.globalColorScheme = cs; - for (int i = 0; i < av.alignment.getGroups().size();i++) - { - SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i); - sg.cs = cs; - if(!showConservation - && !(sg.cs instanceof Blosum62ColourScheme) - && sg.cs instanceof ConservationColourScheme) - { - // remove ConservationColouring from existing Conservation group - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; - } - else if(showConservation && !(sg.cs instanceof ConservationColourScheme)) - { - // add ConservationColouring to new group - Conservation c = sg.getConservation(); - Alignment al = (Alignment) av.getAlignment(); - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth() ); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - sg.cs = new ConservationColourScheme(sg); - } - } + seqCanvas.repaint(); } - else - { - SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)); - if( isNewSelection(sg) ) - { - sg = av.getAlignment().addGroup(); - for (int i=0; i < av.getSelection().size(); i++) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (mouseDragging) { - av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av. - sel.sequenceAt(i)), - (Sequence) av.sel.sequenceAt(i)); - av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i)); + stretchGroup.recalcConservation(); + mouseDragging = false; } - } + if (stretchGroup == null) + { + return; + } - sg.cs = cs; + if(stretchGroup.cs!=null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. + sequences, + stretchGroup.getWidth()); + } - // Selection is made, we only want to change the conservationColour for selected group - if( showConservation - && !(sg.cs instanceof ConservationColourScheme) - && !(sg.cs instanceof Blosum62ColourScheme)) - { - Conservation c = sg.getConservation(); - Alignment al = (Alignment) av.getAlignment(); - - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth() ); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - sg.cs = new ConservationColourScheme(sg); + 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(av.alignment); } - else if( !showConservation && sg.cs instanceof ConservationColourScheme) + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseDraggedDefineMode(MouseEvent evt) { - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; - } - } - repaint(); - } + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq(); - boolean isNewSelection(SequenceGroup sg) - { - if(sg==null) - return true; + if (stretchGroup == null) + { + return; + } - if(sg.getSize()!=av.getSelection().size()) - return true; + if (res > av.alignment.getWidth()) + { + res = av.alignment.getWidth() - 1; + } - for(int i=0; i av.getEndRes()) + { + res = av.getEndRes(); + } + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } - public ColourSchemeI getColourScheme() - { - if(av.getSelection().size()>0) - return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs; - else - return seqCanvas.globalColorScheme; - } + int dragDirection = 0; - public void doMousePressedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int seq = evt.getY()/av.getCharHeight() + av.getStartSeq(); + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } - stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq)); + while ((y != oldSeq) && (oldSeq > 0) && (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); - 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; - } + oldSeq += dragDirection; + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - } + if (stretchGroup.sequences.contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) + { + stretchGroup.addSequence(seq, false); + } - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; + stretchGroup.addSequence(nextSeq, false); + } + } - public void doMouseReleasedDefineMode(MouseEvent evt) - { - changeEndRes = false; - changeStartRes = false; - } + oldSeq = y; + mouseDragging = true; - public void doMouseDraggedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int seq = evt.getY()/av.getCharHeight() + av.getStartSeq(); + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } - if(resav.getEndRes()) - res = av.getEndRes(); + seqCanvas.repaint(); + } - if(changeEndRes) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void doMouseEnteredDefineMode(MouseEvent e) { - if(res>stretchGroup.getStartRes()-1) - stretchGroup.setEndRes( res ); + if (scrollThread != null) + { + scrollThread.running = false; + } } - else if(changeStartRes) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void doMouseExitedDefineMode(MouseEvent e) { - if(res 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(true); + } + else if (mouseDragging && (evt.getX() >= getWidth())) + { + running = ap.scrollRight(false); + } + } + + try + { + Thread.sleep(75); + } + catch (Exception ex) + { + } + } + } + } +}