X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=ca5d7f7be2a2ba74bf6cddd90cc029cb0aeb28e9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=336532cf553ed2508ab0f92c453a0362302c65b5;hpb=85b15d4a71f0bb3240e544a5d6bd320ee5e91856;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index 336532c..ca5d7f7 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 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, 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, @@ -100,9 +99,9 @@ public class SeqPanel extends JPanel implements MouseListener, * Creates a new SeqPanel object. * * @param avp - * DOCUMENT ME! + * DOCUMENT ME! * @param p - * DOCUMENT ME! + * DOCUMENT ME! */ public SeqPanel(AlignViewport av, AlignmentPanel ap) { @@ -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 { @@ -524,7 +528,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -544,7 +548,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -602,7 +606,7 @@ 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 +615,10 @@ public class SeqPanel extends JPanel implements MouseListener, { if (av.followHighlight) { - ap.scrollToPosition(results, false); + if (ap.scrollToPosition(results, false)) + { + seqCanvas.revalidate(); + } } seqCanvas.highlightSearchResults(results); } @@ -626,7 +633,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -688,9 +695,11 @@ 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); + 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) // { @@ -706,23 +715,33 @@ public class SeqPanel extends JPanel implements MouseListener, setToolTipText(tooltipText.toString()); lastTooltip = tooltipText.toString(); } - + } - + } - /* (non-Javadoc) + 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 = (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 p; + 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; } /** @@ -733,11 +752,17 @@ public class SeqPanel extends JPanel implements MouseListener, * @param linkImageURL * @param rpos * @param features - * TODO refactor to Jalview 'utilities' somehow. + * TODO refactor to Jalview 'utilities' somehow. */ - public static void appendFeatures(StringBuffer tooltipText2, + public void appendFeatures(StringBuffer tooltipText2, String linkImageURL, int rpos, SequenceFeature[] features) { + appendFeatures(tooltipText2, linkImageURL, rpos, features, null); + } + + public void appendFeatures(StringBuffer tooltipText2, String string, + int rpos, SequenceFeature[] features, Hashtable minmax) + { String tmpString; if (features != null) { @@ -786,17 +811,20 @@ 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); @@ -826,11 +854,15 @@ public class SeqPanel extends JPanel implements MouseListener, } } } - // TODO: check min/max range for this feature type to decide if - // score should be shown + // check score should be shown if (features[i].getScore() != Float.NaN) { - tooltipText2.append(" Score=" + features[i].getScore()); + 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()); + } } if (features[i].getValue("status") != null) { @@ -858,11 +890,11 @@ public class SeqPanel extends JPanel implements MouseListener, * Set status message in alignment panel * * @param sequence - * aligned sequence object + * aligned sequence object * @param res - * alignment column + * alignment column * @param seq - * index of sequence in alignment + * index of sequence in alignment * @return position of res in sequence */ int setStatusMessage(SequenceI sequence, int res, int seq) @@ -906,7 +938,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -916,8 +948,7 @@ 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(); @@ -935,9 +966,7 @@ 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(); } @@ -1374,7 +1403,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent e) { @@ -1394,7 +1423,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent e) { @@ -1411,24 +1440,26 @@ 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) @@ -1452,13 +1483,14 @@ public class SeqPanel extends JPanel implements MouseListener, { ap.scrollUp(true); } + // TODO Update tooltip for new position. } /** * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMousePressedDefineMode(MouseEvent evt) { @@ -1531,8 +1563,8 @@ 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++) { @@ -1603,7 +1635,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseReleasedDefineMode(MouseEvent evt) { @@ -1612,36 +1644,30 @@ 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; @@ -1653,7 +1679,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseDraggedDefineMode(MouseEvent evt) { @@ -1855,43 +1881,84 @@ 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 = (seqsel != null) ? seqsel.intersect( - av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences - : null) : null; - if (sgroup != null && sgroup.getSize() > 0) + if (av.alignment == null) { - av.setSelectionGroup(sgroup); + jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediatly."); + return; } - else + sgroup = seqsel.intersect(av.alignment, + (av.hasHiddenRows) ? av.hiddenRepSequences : null); + if ((sgroup == null || sgroup.getSize() == 0) + || (colsel == null || colsel.size() == 0)) { - av.setSelectionGroup(null); + // don't copy columns if the region didn't intersect. + copycolsel = false; } - repaint = av.isSelectionGroupChanged(); } - if (av.colSel == null || !av.isColSelChanged()) + 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) { - // Check to see if the current selection is from a previous message - if (colsel == null || colsel.size() == 0) + if (av.colSel != null) { av.colSel.clear(); + repaint=true; } - else + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.colSel == null) { av.colSel = new ColumnSelection(colsel); } - repaint |= av.isColSelChanged(); + else + { + av.colSel.setElementsFrom(colsel); + } } + av.isColSelChanged(true); + repaint = true; + } + if (copycolsel && av.hasHiddenColumns + && (av.colSel == null || av.colSel.getHiddenColumns() == null)) + { + System.err.println("Bad things"); } if (repaint) {