X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1cc87156c7a93ba356bd31c29d6df1c27f9a0b3b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3095c47b22e6b449a3a097ee81cb0fac544097d7;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3095c47..1cc8715 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,36 +1,57 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. + * 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! @@ -92,7 +113,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(""); + StringBuffer tooltipText = new StringBuffer(); String tmpString; @@ -129,8 +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); } @@ -223,42 +243,6 @@ public class SeqPanel extends JPanel implements MouseListener, 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].featureGroup != null - && seqCanvas.fr.featureGroups != null - && seqCanvas.fr.featureGroups - .containsKey(features[i].featureGroup) - && !((Boolean) seqCanvas.fr.featureGroups - .get(features[i].featureGroup)).booleanValue()) - continue; - - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) - { - tmp.addElement(features[i]); - } - } - } - - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; - } - void endEditing() { if (editCommand != null && editCommand.getSize() > 0) @@ -307,7 +291,7 @@ public class SeqPanel extends JPanel implements MouseListener, { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); - seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } @@ -518,26 +502,36 @@ 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; } /** @@ -683,7 +677,9 @@ 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 @@ -694,11 +690,6 @@ 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")) { @@ -714,14 +705,14 @@ public class SeqPanel extends JPanel implements MouseListener, } // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { int rpos; - SequenceFeature[] features = findFeaturesAtRes( + List features = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, - this.ap.seqPanel.seqCanvas.fr.minmax); + this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // { @@ -730,11 +721,13 @@ 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(); } @@ -937,7 +930,7 @@ 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 @@ -950,7 +943,7 @@ 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})); } } @@ -1156,7 +1149,7 @@ 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); } } @@ -1172,7 +1165,7 @@ 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); } @@ -1194,7 +1187,7 @@ 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); } } @@ -1231,7 +1224,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - editCommand.appendEdit(EditCommand.DELETE_GAP, + editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, startres, max, av.getAlignment(), true); } @@ -1249,7 +1242,7 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[] + editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, startres - lastres, av.getAlignment(), true); } } @@ -1285,10 +1278,10 @@ 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, + editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(), true); } @@ -1296,10 +1289,10 @@ public class SeqPanel extends JPanel implements MouseListener, void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, + 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); } @@ -1358,21 +1351,21 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( + List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); seqCanvas.highlightSearchResults(null); } @@ -1425,9 +1418,10 @@ 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; } @@ -1486,16 +1480,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes( + List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); - for (int i = 0; i < allFeatures.length; i++) + for (SequenceFeature sf:allFeatures) { - if (allFeatures[i].links != null) + if (sf.links != null) { - for (int j = 0; j < allFeatures[i].links.size(); j++) + for (int j = 0; j < sf.links.size(); j++) { - links.addElement(allFeatures[i].links.elementAt(j)); + links.addElement(sf.links.elementAt(j)); } } }