X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=97b8669cd1d1c4f6e3aca9907081fe96f477ee03;hb=fb1cdebe4a9d93839c81a2d3eb39e8da9cb83d64;hp=e30be30456316515640352d7c1693f1edbe2e8d1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index e30be30..97b8669 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -22,9 +22,14 @@ import java.awt.*; import java.awt.image.*; import javax.swing.*; -import jalview.analysis.*; import jalview.datamodel.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class IdCanvas extends JPanel { @@ -37,57 +42,85 @@ public class IdCanvas int imgHeight = 0; boolean fastPaint = false; java.util.Vector searchResults; - + FontMetrics fm; + AnnotationLabels labels = null; + AnnotationPanel ap; + Font idfont; + + /** + * Creates a new IdCanvas object. + * + * @param av DOCUMENT ME! + */ public IdCanvas(AlignViewport av) { setLayout(new BorderLayout()); this.av = av; - PaintRefresher.Register(this); + PaintRefresher.Register(this, av.getSequenceSetId()); } + /** + * DOCUMENT ME! + * + * @param gg DOCUMENT ME! + * @param s DOCUMENT ME! + * @param i DOCUMENT ME! + * @param starty DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos) { - int charHeight = av.getCharHeight(); + int xPos = 0; + int panelWidth = getWidth(); + int charHeight = av.charHeight; if ( (searchResults != null) && searchResults.contains(s)) { gg.setColor(Color.black); - gg.fillRect(0, - AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos, - getWidth(), charHeight); + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(), + charHeight); gg.setColor(Color.white); } else if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains(s)) + av.getSelectionGroup().getSequences(null).contains(s)) { gg.setColor(Color.lightGray); - gg.fillRect(0, - AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos, - getWidth(), charHeight); + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(), + charHeight); gg.setColor(Color.white); } else { - gg.setColor(s.getColor()); - gg.fillRect(0, - AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos, - getWidth(), charHeight); + gg.setColor(av.getSequenceColour(s)); + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(), + charHeight); gg.setColor(Color.black); } - String string = s.getName(); + if (av.rightAlignIds) + { + xPos = panelWidth - fm.stringWidth( + s.getDisplayId(av.getShowJVSuffix()) + ) - 4; + } + + gg.drawString(s.getDisplayId(av.getShowJVSuffix()), + xPos, + ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); - if (av.getShowFullId()) + if (av.hasHiddenRows && av.showHiddenMarkers) { - string = s.getDisplayId(); + drawMarker(i, starty, ypos); } - gg.drawString(string, 0, - (AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos + - charHeight) - (charHeight / 5)); } + /** + * DOCUMENT ME! + * + * @param vertical DOCUMENT ME! + */ public void fastPaint(int vertical) { if (gg == null) @@ -136,6 +169,11 @@ public class IdCanvas repaint(); } + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ public void paintComponent(Graphics g) { g.setColor(Color.white); @@ -149,6 +187,8 @@ public class IdCanvas return; } + int oldHeight = imgHeight; + imgHeight = getHeight(); imgHeight -= (imgHeight % av.charHeight); @@ -157,98 +197,278 @@ public class IdCanvas return; } - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); + if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) + { + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); + } + gg = (Graphics2D) image.getGraphics(); //Fill in the background gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - gg.setFont(italic); drawIds(av.getStartSeq(), av.endSeq); g.drawImage(image, 0, 0, this); } + /** + * DOCUMENT ME! + * + * @param starty DOCUMENT ME! + * @param endy DOCUMENT ME! + */ void drawIds(int starty, int endy) { + if (av.seqNameItalics) + { + idfont = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + } + else + { + idfont = av.getFont(); + } + + gg.setFont(idfont); + fm = gg.getFontMetrics(); + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + Color currentColor = Color.white; Color currentTextColor = Color.black; if (av.getWrapAlignment()) { + int maxwidth = av.alignment.getWidth(); + int alheight = av.alignment.getHeight(); + + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + int annotationHeight = 0; + + if (av.showAnnotation) + { + if (ap == null) + { + ap = new AnnotationPanel(av); + } + + annotationHeight = ap.adjustPanelHeight(); + if (labels == null) + { + labels = new AnnotationLabels(av); + } + } + + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } + + int cHeight = alheight * av.charHeight + + hgap + + annotationHeight; + int rowSize = av.getEndRes() - av.getStartRes(); // Draw the rest of the panels - for (int ypos = 2 * av.charHeight, row = av.startRes; - (ypos <= getHeight()) && (row < av.alignment.getWidth()); - ypos += av.chunkHeight, row += rowSize) + for (int ypos = hgap, row = av.startRes; + (ypos <= getHeight()) && (row < maxwidth); + ypos += cHeight, row += rowSize) { - for (int i = starty; i < av.alignment.getHeight(); i++) + for (int i = starty; i < alheight; i++) { SequenceI s = av.alignment.getSequenceAt(i); + if (av.hasHiddenRows) + { + setHiddenFont(s); + } + else + { + gg.setFont(idfont); + } + drawIdString(gg, s, i, 0, ypos); } + + if (labels != null && av.showAnnotation) + { + gg.translate(0, ypos + (alheight * av.charHeight)); + labels.drawComponent(gg, getWidth()); + gg.translate(0, -ypos - (alheight * av.charHeight)); + } } } else { + //No need to hang on to labels if we're not wrapped + labels = null; + + //Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; + + SequenceI sequence; //Now draw the id strings for (int i = starty; i < endy; i++) { + sequence = av.alignment.getSequenceAt(i); + + if (sequence == null) + { + continue; + } + + if (av.hasHiddenRows) + { + setHiddenFont(sequence); + } + // Selected sequence colours if ( (searchResults != null) && - searchResults.contains(av.alignment.getSequenceAt(i))) + searchResults.contains(sequence)) { - gg.setColor(Color.black); currentColor = Color.black; currentTextColor = Color.white; } else if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains( - av.alignment.getSequenceAt(i))) + av.getSelectionGroup().getSequences(null).contains( + sequence)) { currentColor = Color.lightGray; currentTextColor = Color.black; } else { - currentColor = av.alignment.getSequenceAt(i).getColor(); + currentColor = av.getSequenceColour(sequence); currentTextColor = Color.black; } gg.setColor(currentColor); - gg.fillRect(0, - AlignmentUtil.getPixelHeight(starty, i, av.charHeight), - getWidth(), av.charHeight); + gg.fillRect(0, (i - starty) * av.charHeight, getWidth(), + av.charHeight); gg.setColor(currentTextColor); - String string = av.alignment.getSequenceAt(i).getName(); + String string = sequence.getDisplayId(av.getShowJVSuffix()); + + if (av.rightAlignIds) + { + xPos = panelWidth - fm.stringWidth(string) - 4; + } + + gg.drawString(string, xPos, + ( ( (i - starty) * av.charHeight) + av.charHeight) - + (av.charHeight / 5)); - if (av.getShowFullId()) + if (av.hasHiddenRows && av.showHiddenMarkers) { - string = av.alignment.getSequenceAt(i).getDisplayId(); + drawMarker(i, starty, 0); } - gg.drawString(string, 0, - (AlignmentUtil.getPixelHeight(starty, i, av.charHeight) + - av.charHeight) - (av.charHeight / 5)); } - // add a border - gg.setColor(Color.white); - gg.fillRect(getWidth() - 4, 0, 4, getHeight()); } } + void drawMarker(int i, int starty, int yoffset) + { + + SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences; + //Use this method here instead of calling hiddenSeq adjust + //3 times. + int hSize = hseqs.length; + + int hiddenIndex = i; + int lastIndex = i - 1; + int nextIndex = i + 1; + + for (int j = 0; j < hSize; j++) + { + if (hseqs[j] != null) + { + if (j - 1 < hiddenIndex) + { + hiddenIndex++; + } + if (j - 1 < lastIndex) + { + lastIndex++; + } + if (j - 1 < nextIndex) + { + nextIndex++; + } + } + } + + boolean below = (hiddenIndex > lastIndex + 1); + boolean above = (nextIndex > hiddenIndex + 1); + + gg.setColor(Color.blue); + if (below) + { + gg.fillPolygon(new int[] + {getWidth() - av.charHeight, + getWidth() - av.charHeight, + getWidth()}, + new int[] + { + (i - starty) * av.charHeight + yoffset, + (i - starty) * av.charHeight + yoffset + av.charHeight / 4, + (i - starty) * av.charHeight + yoffset + }, 3); + } + if (above) + { + gg.fillPolygon(new int[] + {getWidth() - av.charHeight, + getWidth() - av.charHeight, + getWidth()}, + new int[] + { + (i - starty + 1) * av.charHeight + yoffset, + (i - starty + 1) * av.charHeight + yoffset - + av.charHeight / 4, + (i - starty + 1) * av.charHeight + yoffset + }, 3); + + } + } + + void setHiddenFont(SequenceI seq) + { + Font bold = new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); + + if (av.hiddenRepSequences != null && + av.hiddenRepSequences.containsKey(seq)) + { + gg.setFont(bold); + } + else + { + gg.setFont(idfont); + } + } + + /** + * DOCUMENT ME! + * + * @param found DOCUMENT ME! + */ public void setHighlighted(java.util.Vector found) { searchResults = found;