X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=294b8db964023849c80b70be9564548496649089;hb=2639d90e2b52d49cf586c0b602bc606033c9b8ae;hp=4b774d60cbab3252eaa0868b182136f0545f6bda;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 4b774d6..294b8db 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,25 +20,29 @@ */ package jalview.gui; +import jalview.analysis.AlignSeq; import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.FileFormat; import jalview.io.FormatAdapter; +import jalview.util.Comparison; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.dialogrunner.RunResponse; import java.awt.Color; +import java.awt.Cursor; import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; -import java.awt.Image; -import java.awt.MediaTracker; import java.awt.RenderingHints; import java.awt.Toolkit; import java.awt.datatransfer.StringSelection; @@ -48,11 +52,9 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; -import java.awt.image.BufferedImage; -import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.List; +import java.util.Iterator; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -63,63 +65,74 @@ import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel that holds the labels for alignment annotations, providing + * tooltips, context menus, drag to reorder rows, and drag to adjust panel + * height */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern .compile("<"); - String TOGGLE_LABELSCALE = MessageManager + private static final Font font = new Font("Arial", Font.PLAIN, 11); + + private static final String TOGGLE_LABELSCALE = MessageManager .getString("label.scale_label_to_column"); - String ADDNEW = MessageManager.getString("label.add_new_row"); + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); - String EDITNAME = MessageManager + private static final String EDITNAME = MessageManager .getString("label.edit_label_description"); - String HIDE = MessageManager.getString("label.hide_row"); + private static final String HIDE = MessageManager + .getString("label.hide_row"); - String DELETE = MessageManager.getString("label.delete_row"); + private static final String DELETE = MessageManager + .getString("label.delete_row"); - String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); - String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager + private static final String COPYCONS_SEQ = MessageManager .getString("label.copy_consensus_sequence"); - boolean resizePanel = false; - - Image image; + private final boolean debugRedraw = false; - AlignmentPanel ap; + private AlignmentPanel ap; AlignViewport av; - boolean resizing = false; - - MouseEvent dragEvent; + private MouseEvent dragEvent; - int oldY; + private int oldY; - int selectedRow; + private int selectedRow; private int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - private boolean hasHiddenRows; + private boolean resizePanel = false; + /** - * Creates a new AnnotationLabels object. + * Creates a new AnnotationLabels object * * @param ap - * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@ -127,30 +140,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); - 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 = bi; - addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(ap.getAnnotationPanel()); @@ -220,41 +209,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - boolean fullRepaint = false; - if (evt.getActionCommand().equals(ADDNEW)) + String action = evt.getActionCommand(); + if (ADDNEW.equals(action)) { + /* + * non-returning dialog + */ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, null, new Annotation[ap.av.getAlignment().getWidth()]); - - if (!editLabelDescription(newAnnotation)) - { - return; - } - - ap.av.getAlignment().addAnnotation(newAnnotation); - ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); - fullRepaint = true; + editLabelDescription(newAnnotation, true); } - else if (evt.getActionCommand().equals(EDITNAME)) + else if (EDITNAME.equals(action)) { - String name = aa[selectedRow].label; - editLabelDescription(aa[selectedRow]); - if (!name.equalsIgnoreCase(aa[selectedRow].label)) - { - fullRepaint = true; - } + /* + * non-returning dialog + */ + editLabelDescription(aa[selectedRow], false); } - else if (evt.getActionCommand().equals(HIDE)) + else if (HIDE.equals(action)) { aa[selectedRow].visible = false; } - else if (evt.getActionCommand().equals(DELETE)) + else if (DELETE.equals(action)) { ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); - fullRepaint = true; } - else if (evt.getActionCommand().equals(SHOWALL)) + else if (SHOWALL.equals(action)) { for (int i = 0; i < aa.length; i++) { @@ -263,14 +244,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[i].visible = true; } } - fullRepaint = true; } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + else if (OUTPUT_TEXT.equals(action)) { - new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] { aa[selectedRow] }); + new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + else if (COPYCONS_SEQ.equals(action)) { SequenceI cons = null; if (aa[selectedRow].groupRef != null) @@ -285,68 +264,54 @@ public class AnnotationLabels extends JPanel implements MouseListener, { copy_annotseqtoclipboard(cons); } - } - else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(fullRepaint); - + ap.refresh(true); } /** - * Redraw sensibly. + * Shows a dialog where the annotation name and description may be edited. If + * parameter addNew is true, then on confirmation, a new AlignmentAnnotation + * is added, else an existing annotation is updated. * - * @adjustHeight if true, try to recalculate panel height for visible - * annotations + * @param annotation + * @param addNew */ - protected void refresh(boolean adjustHeight) + void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) { - ap.validateAnnotationDimensions(adjustHeight); - ap.addNotify(); - if (adjustHeight) - { - // sort, repaint, update overview - ap.paintAlignment(true); - } - else - { - // lightweight repaint - ap.repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - boolean editLabelDescription(AlignmentAnnotation annotation) - { - // TODO i18n + String name = MessageManager.getString("label.annotation_name"); + String description = MessageManager + .getString("label.annotation_description"); + String title = MessageManager + .getString("label.edit_annotation_name_description"); EditNameDialog dialog = new EditNameDialog(annotation.label, - annotation.description, " Annotation Name ", - "Annotation Description ", "Edit Annotation Name/Description", - ap.alignFrame); - - if (!dialog.accept) - { - return false; - } - - annotation.label = dialog.getName(); + annotation.description, name, description); - String text = dialog.getDescription(); - if (text != null && text.length() == 0) - { - text = null; - } - annotation.description = text; - - return true; + dialog.showDialog(ap.alignFrame, title, + new RunResponse(JvOptionPane.OK_OPTION) + { + @Override + public void run() + { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + } + }); } @Override @@ -420,7 +385,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // ann.visible = false; // } // } - refresh(true); + ap.refresh(true); } }); pop.add(hideType); @@ -462,9 +427,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -475,8 +440,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // TODO: pass on reference to ap so the view can be updated. aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint( - ap.getAnnotationPanel().getGraphics()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } else { @@ -629,10 +594,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Reorders annotation rows after a drag of a label * * @param evt - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) @@ -647,6 +611,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; + /* + * if dragging to resize instead, start == end + */ if (start != end) { // Swap these annotations @@ -670,31 +637,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseEntered(MouseEvent evt) - { - if (evt.getY() < 10) - { - resizePanel = true; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * Removes the height adjuster image on leaving the panel, unless currently + * dragging it */ @Override public void mouseExited(MouseEvent evt) { - if (dragEvent == null) + if (resizePanel && dragEvent == null) { resizePanel = false; repaint(); @@ -702,10 +651,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * A mouse drag may be either an adjustment of the panel height (if flag + * resizePanel is set on), or a reordering of the annotation rows. The former + * is dealt with by this method, the latter in mouseReleased. * * @param evt - * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) @@ -722,12 +672,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, if ((d.height - dif) > 20) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + ap.annotationScroller + .setPreferredSize(new Dimension(d.width, d.height - dif)); d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.paintAlignment(true); + ap.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); + ap.paintAlignment(true, false); } ap.addNotify(); @@ -739,20 +689,19 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Updates the tooltip as the mouse moves over the labels * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10; + showOrHideAdjuster(evt); getSelectedRow(evt.getY() - getScrollOffset()); - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) { AlignmentAnnotation aa = ap.av.getAlignment() .getAlignmentAnnotation()[selectedRow]; @@ -766,8 +715,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // tooltips desc.append(aa.getDescription(true).trim()); // check to see if the description is an html fragment. - if (desc.length() < 6 - || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) + if (desc.length() < 6 || (desc.substring(0, 6).toLowerCase() + .indexOf("") < 0)) { // clean the description ready for embedding in html desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) @@ -823,6 +772,27 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } + /** + * Shows the height adjuster image if the mouse moves into the top left + * region, or hides it if the mouse leaves the regio + * + * @param evt + */ + protected void showOrHideAdjuster(MouseEvent evt) + { + boolean was = resizePanel; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + + if (resizePanel != was) + { + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR + : Cursor.DEFAULT_CURSOR)); + repaint(); + } + } + @Override public void mouseClicked(MouseEvent evt) { @@ -841,17 +811,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); // process modifiers SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null - || sg == aa[selectedRow].groupRef - || !(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (sg == null || sg == aa[selectedRow].groupRef + || !(Platform.isControlDown(evt) || evt.isShiftDown())) { - if (jalview.util.Platform.isControlDown(evt) - || evt.isShiftDown()) + if (Platform.isControlDown(evt) || evt.isShiftDown()) { // clone a new selection group from the associated group - ap.av.setSelectionGroup(new SequenceGroup( - aa[selectedRow].groupRef)); + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); } else { @@ -878,7 +845,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -893,10 +860,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.getSeqPanel().ap - .getIdPanel() - .highlightSearchResults( - Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + ap.getSeqPanel().ap.getIdPanel() + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -907,8 +873,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // 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())) + if (!(Platform.isControlDown(evt) || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -916,7 +881,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - if (jalview.util.Platform.isControlDown(evt)) + if (Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@ -936,7 +901,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -961,39 +926,38 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); - dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, sq.getSequenceAsString())); + dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, + sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + Iterator it = av.getAlignment().getHiddenColumns() + .getVisContigsIterator(0, sq.getLength(), false); + omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; } int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; - List hiddenCols = av.getColumnSelection().getHiddenColumns(); - if (hiddenCols != null) + if (av.hasHiddenColumns()) { - alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex( - hiddenCols); + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; + if (av.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - hiddenColumns.add(new int[] { region[0], region[1] }); - } + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1046,8 +1010,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, drawComponent(g, false, width); } - private final boolean debugRedraw = false; - /** * Draw the full set of annotation Labels for the alignment at the given * cursor @@ -1089,8 +1051,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap - .getAnnotationPanel().getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) + ? ap.getAnnotationPanel().getVisibleVRange() + : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1133,8 +1096,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (debugRedraw) { - System.out.println("Scroll offset: " + sOffset - + " after vis: " + i); + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); } after = true; } @@ -1172,7 +1135,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, } if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } else { @@ -1186,11 +1150,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, { fontHeight = -8 + (int) h; s = ((float) fontHeight) / (float) ofontH; - Font f = baseFont.deriveFont(AffineTransform - .getScaleInstance(s, s)); + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); g.setFont(f); fm = g.getFontMetrics(); - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } } if (visible) @@ -1207,8 +1172,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(aa[gg]._linecolour); g.drawLine(x, y - graphExtras + 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - + 3); + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } g.setColor(Color.black); @@ -1227,11 +1192,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - if (resizePanel) - { - g.drawImage(image, 2, 0 - getScrollOffset(), this); - } - else if (dragEvent != null && aa != null) + if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), @@ -1250,4 +1211,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, { return scrollOffset; } + + @Override + public void mouseEntered(MouseEvent e) + { + } }