X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1903294140283cfedd325160b1cd6cd3462a2a0c;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e32c5cfdf246cc14ef53fba7c6224ecf45e9e1c8;hpb=5e67396f7f70d20025e8112ce09f2095ebc94584;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index e32c5cf..1903294 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview. * - * 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. + * 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. * - * 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 + * 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 . */ package jalview.gui; @@ -34,7 +33,7 @@ import jalview.structure.*; * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.130 $ */ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, @@ -124,7 +123,7 @@ public class SeqPanel extends JPanel implements MouseListener, addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -169,6 +168,11 @@ public class SeqPanel extends JPanel implements MouseListener, } else { + if (x>seqCanvas.getWidth()+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(); } @@ -199,8 +203,8 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment - .getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); } else { @@ -466,7 +470,7 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; - editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); + editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -475,9 +479,17 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX + getKeyboardNo1(); - editSequence(false, seqCanvas.cursorX); + 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) { @@ -602,7 +614,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (lastMessage == null || !lastMessage.equals(tmp)) { // System.err.println("mouseOver Sequence: "+tmp); - ssm.mouseOverSequence(sequence, index, pos); + ssm.mouseOverSequence(sequence, index, pos, av); } lastMessage = tmp; } @@ -611,7 +623,10 @@ public class SeqPanel extends JPanel implements MouseListener, { if (av.followHighlight) { - ap.scrollToPosition(results, false); + if (ap.scrollToPosition(results, false)) + { + seqCanvas.revalidate(); + } } seqCanvas.highlightSearchResults(results); } @@ -688,9 +703,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.showSequenceFeatures) { int rpos; - SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), rpos = sequence.findPosition(res)); - appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,this.ap.seqPanel.seqCanvas.fr.minmax); + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + rpos = sequence.findPosition(res)); + appendFeatures(tooltipText, linkImageURL.toString(), rpos, features, + this.ap.seqPanel.seqCanvas.fr.minmax); } if (tooltipText.length() == 6) // { @@ -710,7 +727,9 @@ public class SeqPanel extends JPanel implements MouseListener, } } - private Point lastp=null; + + private Point lastp = null; + /* * (non-Javadoc) * @@ -722,15 +741,15 @@ public class SeqPanel extends JPanel implements MouseListener, 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) { + if (!event.isShiftDown() || p == null) + { p = (tooltipText != null && tooltipText.length() > 6) ? new Point( - event.getX() + wdth, event.getY() - 20) - : null; + event.getX() + wdth, event.getY() - 20) : null; } /* * TODO: try to modify position region is not obcured by tooltip */ - return lastp=p; + return lastp = p; } /** @@ -746,10 +765,11 @@ public class SeqPanel extends JPanel implements MouseListener, public void appendFeatures(StringBuffer tooltipText2, String linkImageURL, int rpos, SequenceFeature[] features) { - appendFeatures(tooltipText2,linkImageURL,rpos,features,null); + appendFeatures(tooltipText2, linkImageURL, rpos, features, null); } + public void appendFeatures(StringBuffer tooltipText2, String string, - int rpos, SequenceFeature[] features, Hashtable minmax) + int rpos, SequenceFeature[] features, Hashtable minmax) { String tmpString; if (features != null) @@ -799,17 +819,20 @@ public class SeqPanel extends JPanel implements MouseListener, .getType())) { tmpString = features[i].getDescription(); - int startTag = tmpString.toUpperCase().indexOf(""); + String tmp2up=tmpString.toUpperCase(); + int startTag = tmp2up.indexOf(""); if (startTag > -1) { tmpString = tmpString.substring(startTag + 6); + tmp2up = tmp2up.substring(startTag+6); } - int endTag = tmpString.toUpperCase().indexOf(""); + int endTag = tmp2up.indexOf(""); if (endTag > -1) { tmpString = tmpString.substring(0, endTag); + tmp2up = tmp2up.substring(0, endTag); } - endTag = tmpString.toUpperCase().indexOf(""); + endTag = tmp2up.indexOf(""); if (endTag > -1) { tmpString = tmpString.substring(0, endTag); @@ -840,9 +863,12 @@ public class SeqPanel extends JPanel implements MouseListener, } } // check score should be shown - if (features[i].getScore() != Float.NaN) { - float[][] rng=(minmax==null) ? null : ((float[][])minmax.get(features[i].getType())); - if (rng!=null && rng[0]!=null && rng[0][0]!=rng[0][1]) { + if (features[i].getScore() != Float.NaN) + { + float[][] rng = (minmax == null) ? null : ((float[][]) minmax + .get(features[i].getType())); + if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) + { tooltipText2.append(" Score=" + features[i].getScore()); } } @@ -930,8 +956,7 @@ public class SeqPanel extends JPanel implements MouseListener, // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt - .getX() - - lastMousePress.getX())) + .getX() - lastMousePress.getX())) { int fontSize = av.font.getSize(); @@ -949,9 +974,7 @@ public class SeqPanel extends JPanel implements MouseListener, fontSize = 1; } - av - .setFont(new Font(av.font.getName(), av.font.getStyle(), - fontSize)); + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); av.charWidth = oldWidth; ap.fontChanged(); } @@ -998,11 +1021,11 @@ public class SeqPanel extends JPanel implements MouseListener, if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap - editSequence(false, res); + editSequence(false, false,res); } else { - editSequence(true, res); + editSequence(true, false,res); } mouseDragging = true; @@ -1012,7 +1035,8 @@ public class SeqPanel extends JPanel implements MouseListener, } } - synchronized void editSequence(boolean insertGap, int startres) + //TODO: Make it more clever than many booleans + synchronized void editSequence(boolean insertGap, boolean editSeq, int startres) { int fixedLeft = -1; int fixedRight = -1; @@ -1297,10 +1321,11 @@ public class SeqPanel extends JPanel implements MouseListener, { editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] { seq }, lastres, startres - lastres, av.alignment, true); - } + } } else { + if(!editSeq){ // dragging to the left if (fixedColumns && fixedRight != -1) { @@ -1334,6 +1359,21 @@ public class SeqPanel extends JPanel implements MouseListener, { seq }, startres, max, av.alignment, true); } } + }else{//insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] + { seq }, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres, av.alignment, true); + } + } } } @@ -1425,24 +1465,26 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseClicked(MouseEvent evt) { + SequenceGroup sg = null; SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { - if (av.getSelectionGroup().getSize() == 1 - && av.getSelectionGroup().getEndRes() - - av.getSelectionGroup().getStartRes() < 2) + sg = av.getSelectionGroup(); + if (sg != null && sg.getSize() == 1 + && sg.getEndRes() - sg.getStartRes() < 2) { av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(findRes(evt))); + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt))); if (features != null && features.length > 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), features[0] - .getEnd()); + highlight.addResult(sequence, features[0].getBegin(), + features[0].getEnd()); seqCanvas.highlightSearchResults(highlight); } if (features != null && features.length > 0) @@ -1546,8 +1588,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(res)); + SequenceFeature[] allFeatures = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); for (int i = 0; i < allFeatures.length; i++) { @@ -1627,36 +1669,30 @@ public class SeqPanel extends JPanel implements MouseListener, return; } + stretchGroup.recalcConservation(); // always do this - annotation has own + // state if (stretchGroup.cs != null) { if (stretchGroup.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup - .getSequences(av.hiddenRepSequences), stretchGroup - .getWidth()); - } - - if (stretchGroup.cs instanceof Blosum62ColourScheme - || stretchGroup.cs instanceof PIDColourScheme - || stretchGroup.cs.conservationApplied() - || stretchGroup.cs.getThreshold() > 0) - { - stretchGroup.recalcConservation(); + ((ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getWidth()); } if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup - .getName()); + SliderPanel.setConservationSlider(ap, stretchGroup.cs, + stretchGroup.getName()); } else { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup - .getName()); + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, + stretchGroup.getName()); } - PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); } + PaintRefresher.Refresh(this, av.getSequenceSetId()); + ap.paintAlignment(true); changeEndRes = false; changeStartRes = false; @@ -1870,62 +1906,82 @@ public class SeqPanel extends JPanel implements MouseListener, { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... - if (av == source) + // TODO: extend config options to allow user to control if selections may be + // shared between viewports. + if (av == source + || !av.followSelection + || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + || (source instanceof AlignViewport && ((AlignViewport) source) + .getSequenceSetId().equals(av.getSequenceSetId()))) { return; } // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - boolean repaint = false; - if (av.followSelection) + // rules are: colsel is copied if there is a real intersection between + // sequence selection + boolean repaint = false, copycolsel = true; + // if (!av.isSelectionGroupChanged(false)) { - if (av.selectionGroup == null || !av.isSelectionGroupChanged()) + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize()>0) { - SequenceGroup sgroup = null; - if (seqsel != null) + if (av.alignment == null) { - if (av.alignment==null) - { - jalview.bin.Cache.log.warn("alignviewport av SeqSetId="+av.getSequenceSetId()+" ViewId="+av.getViewId()+" 's alignment is NULL! returning immediatly."); - return; - } - sgroup = seqsel.intersect(av.alignment, - (av.hasHiddenRows) ? av.hiddenRepSequences : null); + jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediatly."); + return; } - if (sgroup != null && sgroup.getSize() > 0) + sgroup = seqsel.intersect(av.alignment, + (av.hasHiddenRows) ? av.hiddenRepSequences : null); + if ((sgroup == null || sgroup.getSize() == 0) + || (colsel == null || colsel.size() == 0)) { - av.setSelectionGroup(sgroup); + // don't copy columns if the region didn't intersect. + copycolsel = false; } - else + } + 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.colSel != null) { - av.setSelectionGroup(null); + av.colSel.clear(); + repaint=true; } - repaint = av.isSelectionGroupChanged(); } - if (av.colSel == null || !av.isColSelChanged()) + else { - // the current selection is unset or from a previous message - // so import the new colsel. - if (colsel == null || colsel.size() == 0) + // TODO: shift colSel according to the intersecting sequences + if (av.colSel == null) { - if (av.colSel!=null) - { - av.colSel.clear(); - } + av.colSel = new ColumnSelection(colsel); } else { - if (av.colSel == null) - { - av.colSel = new ColumnSelection(colsel); - } else { - av.colSel.setElementsFrom(colsel); - } + av.colSel.setElementsFrom(colsel); } - repaint |= av.isColSelChanged(); } + av.isColSelChanged(true); + repaint = true; } - if (av.hasHiddenColumns && (av.colSel==null || av.colSel.getHiddenColumns()==null)) + if (copycolsel && av.hasHiddenColumns + && (av.colSel == null || av.colSel.getHiddenColumns() == null)) { System.err.println("Bad things"); }