X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=8a377cce7efedb4464e05f3e38a369b1f08b084a;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=1884a08633aa7c2dae4cf0e7448bc48f81b7a181;hpb=6951479b7dc56bd022ce2c370b7f88b5571004fd;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 1884a08..8a377cc 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,22 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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. - * - * 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 - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . */ - package jalview.appletgui; import java.util.*; @@ -26,28 +24,41 @@ import java.awt.event.*; import jalview.datamodel.*; -public class AnnotationLabels - extends Panel implements ActionListener, MouseListener, MouseMotionListener +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; @@ -68,24 +79,28 @@ public class AnnotationLabels 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 = -1; + int row = -2; AlignmentAnnotation[] aa = ap.av.alignment.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) { @@ -103,9 +118,8 @@ public class AnnotationLabels if (evt.getActionCommand().equals(ADDNEW)) { - AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", - null, - new Annotation[ap.av.alignment.getWidth()]); + AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null, + new Annotation[ap.av.alignment.getWidth()]); if (!editLabelDescription(newAnnotation)) { @@ -127,17 +141,17 @@ public class AnnotationLabels { for (int i = 0; i < aa.length; i++) { - aa[i].visible = (aa[i].annotations==null) ? false : true; + aa[i].visible = (aa[i].annotations == null) ? false : true; } } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); + 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); + 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)) @@ -157,19 +171,26 @@ public class AnnotationLabels boolean editLabelDescription(AlignmentAnnotation annotation) { - EditNameDialog dialog = new EditNameDialog( - annotation.label, - annotation.description, - " Annotation Label", - "Annotation Description", - ap.alignFrame, - "Edit Annotation Name / Description", - 500, 100); + 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; } @@ -186,15 +207,13 @@ public class AnnotationLabels { if (tooltip == null) { - tooltip = new Tooltip(ap.av.alignment. - getAlignmentAnnotation()[row]. - description, - this); + tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row] + .getDescription(true), this); } else { - tooltip.setTip(ap.av.alignment. - getAlignmentAnnotation()[row].description); + tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row] + .getDescription(true)); } } else if (tooltip != null) @@ -205,19 +224,24 @@ public class AnnotationLabels } public void mouseDragged(MouseEvent evt) - {} + { + } public void mouseClicked(MouseEvent evt) - {} + { + } public void mouseReleased(MouseEvent evt) - {} + { + } public void mouseEntered(MouseEvent evt) - {} + { + } public void mouseExited(MouseEvent evt) - {} + { + } public void mousePressed(MouseEvent evt) { @@ -230,15 +254,31 @@ public class AnnotationLabels 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); - item = new MenuItem(SHOWALL); - item.addActionListener(this); - popup.add(item); + if (hasHiddenRows) { + item = new MenuItem(SHOWALL); + item.addActionListener(this); + popup.add(item); + } this.add(popup); item = new MenuItem(OUTPUT_TEXT); item.addActionListener(this); @@ -248,8 +288,7 @@ public class AnnotationLabels { popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); + "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus()); cbmi.addItemListener(new ItemListener() { @@ -271,8 +310,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void copy_annotseqtoclipboard(SequenceI sq) { @@ -281,21 +321,20 @@ public class AnnotationLabels return; } jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer(); - jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" + - sq.getStart() + "\t" + - sq.getEnd() + "\t" + - sq.getSequenceAsString() + "\n"); + 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 i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) { - int[] region = (int[]) - av.getColumnSelection().getHiddenColumns().elementAt(i); + int[] region = (int[]) av.getColumnSelection().getHiddenColumns() + .elementAt(i); - jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[] - {region[0], - region[1]}); + jalview.appletgui.AlignFrame.copiedHiddenColumns + .addElement(new int[] + { region[0], region[1] }); } } } @@ -328,35 +367,26 @@ public class AnnotationLabels g.setColor(Color.black); AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int y = g.getFont().getSize(); - int x = 0; + 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; - if (aa[i].graph > 0) - { - y += (aa[i].height / 3); - } + y += aa[i].height; + offset = -(aa[i].height-fy)/2; - g.drawString(aa[i].label, x, y); - - if (aa[i].graph > 0) - { - y += (2 * aa[i].height / 3); - } - else - { - y += aa[i].height; - } + g.drawString(aa[i].label, x, y+offset); } } }