X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=5d3df1a4484101494ab297d909fafbafcb0f2c93;hb=53a90a961a55fad88199165bdc4c665ba90c28b3;hp=648c3a22e0bbe65a8ad50984fb91cd6c05606ca5;hpb=3eef76298c55f3def21eed2516b5ace4405bed0a;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 648c3a2..5d3df1a 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,39 +1,61 @@ /* - * 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 - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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 + * 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 . + * + * 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 java.util.*; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResults; +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.util.MessageManager; + +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 java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.SequenceAnnotationReport; -import jalview.schemes.*; -import jalview.structure.*; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision: 1.130 $ */ @@ -88,8 +110,10 @@ public class SeqPanel extends JPanel implements MouseListener, StringBuffer keyboardNo2; java.net.URL linkImageURL; + private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(""); + + StringBuffer tooltipText = new StringBuffer(); String tmpString; @@ -99,7 +123,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * Creates a new SeqPanel object. - * + * * @param avp * DOCUMENT ME! * @param p @@ -108,7 +132,7 @@ public class SeqPanel extends JPanel implements MouseListener, public SeqPanel(AlignViewport av, AlignmentPanel ap) { linkImageURL = getClass().getResource("/images/link.gif"); - seqARep=new SequenceAnnotationReport(linkImageURL.toString()); + seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -126,7 +150,7 @@ public class SeqPanel extends JPanel implements MouseListener, addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance); + ssm = av.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -171,10 +195,11 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - if (x>seqCanvas.getWidth()+seqCanvas.getWidth()) + if (x > seqCanvas.getWidth() + seqCanvas.getWidth()) { - // make sure we calculate relative to visible alignment, rather than right-hand gutter - 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(); } @@ -206,13 +231,13 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), - av.getAlignment().getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() + .getHeight() - 1); } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), - av.getAlignment().getHeight() - 1); + seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + .getAlignment().getHeight() - 1); } return seq; @@ -226,8 +251,9 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int i = 0; i < features.length; i++) { - if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) + if (av.getFeaturesDisplayed() == null + || !av.getFeaturesDisplayed().containsKey( + features[i].getType())) { continue; } @@ -238,7 +264,9 @@ public class SeqPanel extends JPanel implements MouseListener, .containsKey(features[i].featureGroup) && !((Boolean) seqCanvas.fr.featureGroups .get(features[i].featureGroup)).booleanValue()) + { continue; + } if ((features[i].getBegin() <= res) && (features[i].getEnd() >= res)) @@ -300,10 +328,9 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorPosition() { - SequenceI sequence = av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); - seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } @@ -311,7 +338,8 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() + && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); @@ -395,8 +423,7 @@ public class SeqPanel extends JPanel implements MouseListener, void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); if (av.getSelectionGroup() != null) { @@ -486,12 +513,13 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); } - void insertNucAtCursor(boolean group,String nuc){ - groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; - editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); - 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) @@ -513,31 +541,41 @@ public class SeqPanel extends JPanel implements MouseListener, int getKeyboardNo1() { - if (keyboardNo1 == null) - return 1; - else + try + { + if (keyboardNo1 != null) + { + int value = Integer.parseInt(keyboardNo1.toString()); + keyboardNo1 = null; + return value; + } + } catch (Exception x) { - int value = Integer.parseInt(keyboardNo1.toString()); - keyboardNo1 = null; - return value; } + keyboardNo1 = null; + return 1; } int getKeyboardNo2() { - if (keyboardNo2 == null) - return 1; - else + try + { + if (keyboardNo2 != null) + { + int value = Integer.parseInt(keyboardNo2.toString()); + keyboardNo2 = null; + return value; + } + } catch (Exception x) { - int value = Integer.parseInt(keyboardNo2.toString()); - keyboardNo2 = null; - return value; } + keyboardNo2 = null; + return 1; } /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -558,7 +596,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -632,7 +670,7 @@ public class SeqPanel extends JPanel implements MouseListener, { if (ap.scrollToPosition(results, false)) { - seqCanvas.revalidate(); + seqCanvas.revalidate(); } } seqCanvas.highlightSearchResults(results); @@ -647,7 +685,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -678,7 +716,9 @@ public class SeqPanel extends JPanel implements MouseListener, pos = setStatusMessage(sequence, res, seq); if (ssm != null && pos > -1) + { mouseOverSequence(sequence, res, pos); + } tooltipText.setLength(6); // Cuts the buffer back to @@ -689,11 +729,6 @@ public class SeqPanel extends JPanel implements MouseListener, { if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) { - if (tooltipText.length() > 6) - { - tooltipText.append("
"); - } - if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) { @@ -715,7 +750,7 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceFeature[] features = findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); - seqARep.appendFeatures(tooltipText, rpos, features, + seqARep.appendFeatures(tooltipText, rpos, features, this.ap.seqPanel.seqCanvas.fr.minmax); } if (tooltipText.length() == 6) // @@ -725,11 +760,13 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - tooltipText.append(""); if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString())) { - setToolTipText(tooltipText.toString()); + String formatedTooltipText = JvSwingUtils.wrapTooltip(true, + tooltipText.toString()); + // String formatedTooltipText = tooltipText.toString(); + setToolTipText(formatedTooltipText); lastTooltip = tooltipText.toString(); } @@ -761,12 +798,11 @@ public class SeqPanel extends JPanel implements MouseListener, return lastp = p; } - String lastTooltip; /** * Set status message in alignment panel - * + * * @param sequence * aligned sequence object * @param res @@ -814,7 +850,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -892,11 +928,11 @@ public class SeqPanel extends JPanel implements MouseListener, if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap - editSequence(false, false,res); + editSequence(false, false, res); } else { - editSequence(true, false,res); + editSequence(true, false, res); } mouseDragging = true; @@ -906,8 +942,9 @@ public class SeqPanel extends JPanel implements MouseListener, } } - //TODO: Make it more clever than many booleans - synchronized void editSequence(boolean insertGap, boolean editSeq, 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; @@ -932,7 +969,7 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand("Edit Group"); + editCommand = new EditCommand(MessageManager.getString("action.edit_group")); } } else @@ -945,7 +982,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand("Edit " + label); + editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); } } @@ -1084,8 +1121,8 @@ public class SeqPanel extends JPanel implements MouseListener, { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av.getColumnSelection() - .getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av + .getColumnSelection().getHiddenBoundaryRight(startres))) { endEditing(); return; @@ -1094,7 +1131,8 @@ public class SeqPanel extends JPanel implements MouseListener, int alWidth = av.getAlignment().getWidth(); if (av.hasHiddenRows()) { - int hwidth = av.getAlignment().getHiddenSequences().getWidth(); + int hwidth = av.getAlignment().getHiddenSequences() + .getWidth(); if (hwidth > alWidth) { alWidth = hwidth; @@ -1150,7 +1188,7 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, + editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres - lastres, av.getAlignment(), true); } } @@ -1166,7 +1204,7 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, + editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres - startres, av.getAlignment(), true); } @@ -1188,61 +1226,65 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] + editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, startres - lastres, av.getAlignment(), true); - } + } } else { - if(!editSeq){ - // dragging to the left - if (fixedColumns && fixedRight != -1) + if (!editSeq) { - for (int j = lastres; j > startres; j--) + // dragging to the left + if (fixedColumns && fixedRight != -1) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + for (int j = lastres; j > startres; j--) { - endEditing(); - break; + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + { + endEditing(); + break; + } + deleteChar(startres, new SequenceI[] + { seq }, fixedRight); + } + } + else + { + // could be a keyboard edit trying to delete none gaps + int max = 0; + for (int m = startres; m < lastres; m++) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + { + break; + } + max++; + } + + if (max > 0) + { + editCommand.appendEdit(Action.DELETE_GAP, + new SequenceI[] + { seq }, startres, max, av.getAlignment(), true); } - 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++) + {// insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + for (int j = lastres; j < startres; j++) { - break; + insertChar(j, new SequenceI[] + { seq }, fixedRight); } - max++; } - - if (max > 0) + else { - editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.getAlignment(), true); + editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), 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.getAlignment(), true); - } - } } } @@ -1275,27 +1317,27 @@ public class SeqPanel extends JPanel implements MouseListener, } } - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, + editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(), - true); + editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, + av.getAlignment(), true); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(), - true); + editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, + editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, av.getAlignment(), true); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ @@ -1316,7 +1358,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ @@ -1375,18 +1417,33 @@ public class SeqPanel extends JPanel implements MouseListener, e.consume(); if (e.getWheelRotation() > 0) { - ap.scrollUp(false); + if (e.isShiftDown()) + { + ap.scrollRight(true); + + } + else + { + ap.scrollUp(false); + } } else { - ap.scrollUp(true); + if (e.isShiftDown()) + { + ap.scrollRight(false); + } + else + { + ap.scrollUp(true); + } } // TODO Update tooltip for new position. } /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1400,9 +1457,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.wrapAlignment && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Cannot edit annotations in wrapped view.", - "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.cannot_edit_annotations_in_wrapped_view"), + MessageManager.getString("label.wrapped_view_no_edit"), + JOptionPane.WARNING_MESSAGE); return; } @@ -1531,7 +1589,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1546,11 +1604,8 @@ public class SeqPanel extends JPanel implements MouseListener, // state if (stretchGroup.cs != null) { - if (stretchGroup.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged( - stretchGroup,av.getHiddenRepSequences()); - } + stretchGroup.cs.alignmentChanged(stretchGroup, + av.getHiddenRepSequences()); if (stretchGroup.cs.conservationApplied()) { @@ -1574,7 +1629,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1640,7 +1695,8 @@ public class SeqPanel extends JPanel implements MouseListener, dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight())) + while ((y != oldSeq) && (oldSeq > -1) + && (y < av.getAlignment().getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -1784,7 +1840,8 @@ public class SeqPanel extends JPanel implements MouseListener, // shared between viewports. if (av == source || !av.followSelection - || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + || (av.isSelectionGroupChanged(false) || av + .isColSelChanged(false)) || (source instanceof AlignViewport && ((AlignViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))) { @@ -1798,7 +1855,7 @@ public class SeqPanel extends JPanel implements MouseListener, // if (!av.isSelectionGroupChanged(false)) { SequenceGroup sgroup = null; - if (seqsel != null && seqsel.getSize()>0) + if (seqsel != null && seqsel.getSize() > 0) { if (av.getAlignment() == null) { @@ -1836,7 +1893,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getColumnSelection() != null) { av.getColumnSelection().clear(); - repaint=true; + repaint = true; } } else @@ -1854,8 +1911,10 @@ public class SeqPanel extends JPanel implements MouseListener, av.isColSelChanged(true); repaint = true; } - if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null)) + if (copycolsel + && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection() + .getHiddenColumns() == null)) { System.err.println("Bad things"); }