-\r
-package jalview.appletgui;\r
-\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationLabels extends Panel\r
-{\r
- boolean active = false;\r
- Image image;\r
- AlignmentPanel ap ;\r
- boolean resizing = false;\r
- int oldY, mouseX;\r
- static String ADDNEW = "Add new row";\r
- static String HIDE = "Hide this row";\r
- static String DELETE = "Delete this row";\r
- static String SHOWALL="Show all hidden rows";\r
- int selectedRow = 0;\r
- int scrollOffset = 0;\r
-\r
- public AnnotationLabels(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- setLayout(null);\r
-\r
- java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- if (url != null)\r
- image = java.awt.Toolkit.getDefaultToolkit().getImage(url);\r
-\r
- try\r
- {\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- }\r
- catch (Exception ex) {}\r
- }\r
-\r
- public void setScrollOffset(int y)\r
- {\r
- scrollOffset = y;\r
- repaint();\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- drawComponent(g);\r
- }\r
-\r
- public void drawComponent(Graphics g)\r
- {\r
- FontMetrics fm = g.getFontMetrics(g.getFont());\r
- g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\r
-\r
- g.translate(0, scrollOffset);\r
- g.setColor(Color.black);\r
-\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\r
- if(aa!=null)\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- x = getSize().width - fm.stringWidth(aa[i].label)-3;\r
-\r
- if(aa[i].isGraph)\r
- y+=(aa[i].height/3);\r
-\r
- g.drawString(aa[i].label, x, y);\r
-\r
- if(aa[i].isGraph)\r
- y+=(2*aa[i].height/3);\r
- else\r
- y+=aa[i].height;\r
- }\r
-\r
- if (active)\r
- {\r
- if (image != null)\r
- g.drawImage(image, 2, 0, this);\r
- }\r
-\r
- if (aa == null || aa.length<1)\r
- {\r
- g.drawString("Right click", 2, 8);\r
- g.drawString("to add annotation", 2, 18);\r
- }\r
-\r
-\r
-\r
- }\r
-\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Vector;
+
+public class AnnotationLabels extends Panel implements ActionListener,
+ MouseListener, MouseMotionListener
+{
+ Image image;
+
+ boolean active = false;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ boolean resizing = false;
+
+ int oldY, mouseX;
+
+ static String ADDNEW = "Add New Row";
+
+ static String EDITNAME = "Edit Label/Description";
+
+ static String HIDE = "Hide This Row";
+
+ static String SHOWALL = "Show All Hidden Rows";
+
+ static String OUTPUT_TEXT = "Show Values In Textbox";
+
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
+ int scrollOffset = 0;
+
+ int selectedRow = -1;
+
+ Tooltip tooltip;
+
+ private boolean hasHiddenRows;
+
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ setLayout(null);
+
+ /**
+ * this retrieves the adjustable height glyph from resources. we don't use
+ * it at the moment. java.net.URL url =
+ * getClass().getResource("/images/idwidth.gif"); Image temp = null;
+ *
+ * if (url != null) { temp =
+ * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
+ *
+ * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
+ * mt.waitForID(0); } catch (Exception ex) { }
+ *
+ * BufferedImage bi = new BufferedImage(temp.getHeight(this),
+ * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
+ * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
+ * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
+ */
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ }
+
+ public AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public void setScrollOffset(int y, boolean repaint)
+ {
+ scrollOffset = y;
+ if (repaint)
+ {
+ repaint();
+ }
+ }
+
+ /**
+ *
+ * @param y
+ * @return -2 if no rows are visible at all, -1 if no visible rows were
+ * selected
+ */
+ int getSelectedRow(int y)
+ {
+ int row = -2;
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ if (aa == null)
+ {
+ return row;
+ }
+ int height = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ row = -1;
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+ height += aa[i].height;
+ if (y < height)
+ {
+ row = i;
+ break;
+ }
+ }
+
+ return row;
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+ new Annotation[ap.av.getAlignment().getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ aa[i].visible = (aa[i].annotations == null) ? false : true;
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+ ap.alignFrame);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+ + " - " + aa[selectedRow].label, 500, 100);
+ cap.setText(aa[selectedRow].toString());
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
+
+ }
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
+ ap.annotationPanel.adjustPanelHeight();
+ setSize(getSize().width, ap.annotationPanel.getSize().height);
+ ap.validate();
+ ap.paintAlignment(true);
+ }
+
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+ + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, " Annotation Label",
+ "Annotation Description", ap.alignFrame,
+ "Edit Annotation Name / Description", 500, 180, false);
+
+ Panel empty = new Panel(new FlowLayout());
+ empty.add(padGaps);
+ dialog.add(empty);
+ dialog.pack();
+
+ dialog.setVisible(true);
+
+ if (dialog.accept)
+ {
+ annotation.label = dialog.getName();
+ annotation.description = dialog.getDescription();
+ annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+ repaint();
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+
+ }
+
+ boolean resizePanel = false;
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ int row = getSelectedRow(evt.getY() + scrollOffset);
+
+ if (row > -1)
+ {
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().getAlignmentAnnotation()[row]
+ .getDescription(true),
+ true, "\n");
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(phb.getNonHtmlContent(), this);
+ }
+ else
+ {
+ tooltip.setTip(phb.getNonHtmlContent());
+ }
+ }
+ else if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ }
+
+ /**
+ * curent drag position
+ */
+ MouseEvent dragEvent = null;
+
+ /**
+ * flag to indicate drag events should be ignored
+ */
+ private boolean dragCancelled = false;
+
+ /**
+ * clear any drag events in progress
+ */
+ public void cancelDrag()
+ {
+ dragEvent = null;
+ dragCancelled = true;
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (dragCancelled)
+ {
+ return;
+ }
+ ;
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
+ .getSize(), f = ap.seqPanelHolder.getSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
+
+ if ((d.height - dif) > 20 && (f.height + dif) > 20)
+ {
+ ap.annotationPanel.setSize(d.width, d.height - dif);
+ setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
+ d.height - dif));
+ ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
+ - dif));
+ ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
+ av.calcPanelHeight());
+ f.height += dif;
+ ap.seqPanelHolder.setPreferredSize(f);
+ ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.validate();
+ // ap.paintAlignment(true);
+ ap.addNotify();
+ }
+
+ }
+ else
+ {
+ int diff;
+ if ((diff = 6 - evt.getY()) > 0)
+ {
+ // nudge scroll up
+ ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
+ ap.adjustmentValueChanged(null);
+
+ }
+ else if ((0 < (diff = 6
+ - ap.annotationSpaceFillerHolder.getSize().height
+ + evt.getY())))
+ {
+ // nudge scroll down
+ ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
+ ap.adjustmentValueChanged(null);
+ }
+ repaint();
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (!resizePanel && !dragCancelled)
+ {
+ int start = selectedRow;
+
+ int end = getSelectedRow(evt.getY() + scrollOffset);
+
+ if (start > -1 && start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+ }
+ resizePanel = false;
+ dragEvent = null;
+ dragCancelled = false;
+ repaint();
+ ap.annotationPanel.repaint();
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10 && evt.getX() < 14)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ dragCancelled = false;
+
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ }
+ else
+ {
+ if (!resizePanel)
+ {
+ dragEvent = null;
+ }
+ }
+ repaint();
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ oldY = evt.getY();
+ if (resizePanel)
+ {
+ return;
+ }
+ dragCancelled = false;
+ // todo: move below to mouseClicked ?
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
+
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < 0)
+ {
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ // add the rest if there are actually rows to show
+ item = new MenuItem(EDITNAME);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(HIDE);
+ item.addActionListener(this);
+ popup.add(item);
+
+ /*
+ * Hide all <label>:
+ */
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ final String label = aa[selectedRow].label;
+ MenuItem hideType = new MenuItem(
+ MessageManager.getString("label.hide_all") + " " + label);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ refresh();
+ }
+ });
+ popup.add(hideType);
+ }
+ }
+
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ item = new MenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ popup.addSeparator();
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.paintAlignment(true);
+ }
+ });
+ popup.add(cbmi);
+ if (aaa.groupRef != null)
+ {
+ final CheckboxMenuItem chist = new CheckboxMenuItem(
+ MessageManager
+ .getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(chist);
+ final CheckboxMenuItem cprofl = new CheckboxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+
+ popup.add(cprofl);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager
+ .getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(true);
+ aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
+ }
+ else
+ {
+ final CheckboxMenuItem chist = new CheckboxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.showConsensusHistogram.setState(chist
+ .getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(chist);
+ final CheckboxMenuItem cprof = new CheckboxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprof);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
+ av.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
+ }
+
+ item = new MenuItem(COPYCONS_SEQ);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ }
+ }
+ popup.show(this, evt.getX(), evt.getY());
+ }
+ else
+ {
+ // selection action.
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
+ {
+ if (evt.getClickCount() >= 2)
+ {
+ // todo: make the ap scroll to the selection - not necessary, first
+ // click highlights/scrolls, second selects
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null
+ || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ if (jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown())
+ {
+ // clone a new selection group from the associated group
+ ap.av.setSelectionGroup(new SequenceGroup(
+ aa[selectedRow].groupRef));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(aa[selectedRow].groupRef
+ .getSequences(null));
+ }
+ return;
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ if (evt.getClickCount() == 1)
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(Arrays
+ .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
+ {
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ else
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ }
+ else
+ {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ ap.av.setSelectionGroup(sg);
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+
+ }
+ }
+
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void copy_annotseqtoclipboard(SequenceI sq)
+ {
+ if (sq == null || sq.getLength() < 1)
+ {
+ return;
+ }
+ jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+ jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+ + sq.getStart() + "\t" + sq.getEnd() + "\t"
+ + sq.getSequenceAsString() + "\n");
+ if (av.hasHiddenColumns())
+ {
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
+ {
+ jalview.appletgui.AlignFrame.copiedHiddenColumns
+ .addElement(new int[] { region[0], region[1] });
+ }
+ }
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ int w = getSize().width;
+ int h = getSize().height;
+ if (image == null || w != image.getWidth(this)
+ || h != image.getHeight(this))
+ {
+ image = createImage(w, ap.annotationPanel.getSize().height);
+ }
+
+ drawComponent(image.getGraphics(), w);
+ g.drawImage(image, 0, 0, this);
+ }
+
+ public void drawComponent(Graphics g, int width)
+ {
+ g.setFont(av.getFont());
+ FontMetrics fm = g.getFontMetrics(av.getFont());
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+
+ g.translate(0, -scrollOffset);
+ g.setColor(Color.black);
+
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int y = 0, fy = g.getFont().getSize();
+ int x = 0, offset;
+
+ if (aa != null)
+ {
+ hasHiddenRows = false;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible)
+ {
+ hasHiddenRows = true;
+ continue;
+ }
+
+ x = width - fm.stringWidth(aa[i].label) - 3;
+
+ y += aa[i].height;
+ offset = -(aa[i].height - fy) / 2;
+
+ g.drawString(aa[i].label, x, y + offset);
+ }
+ }
+ g.translate(0, +scrollOffset);
+ if (resizePanel)
+ {
+ g.setColor(Color.red);
+ g.setPaintMode();
+ g.drawLine(2, 8, 5, 2);
+ g.drawLine(5, 2, 8, 8);
+ }
+ else if (!dragCancelled && dragEvent != null && aa != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY());
+ }
+
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
+ {
+ g.setColor(Color.black);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff