X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=40621373af93fc9b88d67dcc9c084c65283fce3d;hb=4c132b37c867a60959dae032addd78892d996345;hp=4e181b3743c7cb6f4a16db82d87bb7ffcdc9d3ae;hpb=537da9c65518c52985308b67c499fe6a60a607ce;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 4e181b3..4062137 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -25,6 +25,7 @@ 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; @@ -41,8 +42,6 @@ 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; @@ -52,10 +51,9 @@ 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.Iterator; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -73,9 +71,16 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - // width in pixels within which height adjuster arrows are shown and active + /** + * 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("<"); @@ -105,10 +110,6 @@ public class AnnotationLabels extends JPanel private static final String COPYCONS_SEQ = MessageManager .getString("label.copy_consensus_sequence"); - private static Image adjusterImage; - - private static int adjusterImageHeight; - private final boolean debugRedraw = false; private AlignmentPanel ap; @@ -134,15 +135,11 @@ public class AnnotationLabels extends JPanel */ public AnnotationLabels(AlignmentPanel ap) { + this.ap = ap; av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); - if (adjusterImage == null) - { - loadAdjusterImage(); - } - addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(ap.getAnnotationPanel()); @@ -154,37 +151,6 @@ public class AnnotationLabels extends JPanel } /** - * Loads the gif for the panel height adjustment - */ - protected void loadAdjusterImage() - { - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; - - if (url != null) - { - temp = 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); - adjusterImage = bi; - adjusterImageHeight = bi.getHeight(); - } - - /** * DOCUMENT ME! * * @param y @@ -243,41 +209,33 @@ public class AnnotationLabels extends JPanel 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++) { @@ -286,13 +244,12 @@ public class AnnotationLabels extends JPanel aa[i].visible = true; } } - fullRepaint = true; } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + else if (OUTPUT_TEXT.equals(action)) { 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) @@ -307,46 +264,54 @@ public class AnnotationLabels extends JPanel { copy_annotseqtoclipboard(cons); } - } - else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.refresh(fullRepaint); - + ap.refresh(true); } /** - * DOCUMENT ME! + * 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. * - * @param e - * DOCUMENT ME! + * @param annotation + * @param addNew */ - boolean editLabelDescription(AlignmentAnnotation annotation) + void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) { - // 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 Runnable() + { + @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 @@ -816,12 +781,13 @@ public class AnnotationLabels extends JPanel protected void showOrHideAdjuster(MouseEvent evt) { boolean was = resizePanel; - resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; if (resizePanel != was) { - setCursor(Cursor.getPredefinedCursor( - resizePanel ? Cursor.S_RESIZE_CURSOR + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); repaint(); } @@ -968,8 +934,9 @@ public class AnnotationLabels extends JPanel Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getAlignment().getHiddenColumns() - .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 }; @@ -985,12 +952,12 @@ public class AnnotationLabels extends JPanel Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (av.hasHiddenColumns()) { - hiddenColumns = av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy(); + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1225,11 +1192,7 @@ public class AnnotationLabels extends JPanel } } - if (resizePanel) - { - // g.drawImage(adjusterImage, 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(),