X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=484173cf5564e0a081dd51c40c93ab28a09d348b;hb=b2829c5d7e7815e5e261d39964ade91ed5225510;hp=cd7b0b77d8733a2c8d72d688c1a19ff0849c1042;hpb=aad3640b07f836362df7ea025fa09127a0a06145;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index cd7b0b7..484173c 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -63,10 +63,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI List searchResults; - FontMetrics fm; - - AnnotationLabels labels = null; - AnnotationPanel ap; private Font idfont; @@ -88,7 +84,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI /** * DOCUMENT ME! * - * @param gg + * @param g * DOCUMENT ME! * @param hiddenRows * true - check and display hidden row marker if need be @@ -101,7 +97,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI * @param ypos * DOCUMENT ME! */ - public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s, + public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s, int i, int starty, int ypos) { int xPos = 0; @@ -110,39 +106,40 @@ public class IdCanvas extends JPanel implements ViewportListenerI if ((searchResults != null) && searchResults.contains(s)) { - gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.black); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(s)) { - gg.setColor(Color.lightGray); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.lightGray); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else { - gg.setColor(av.getSequenceColour(s)); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(av.getSequenceColour(s)); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.black); + g.setColor(Color.black); } if (av.isRightAlignIds()) { + FontMetrics fm = g.getFontMetrics(); xPos = panelWidth - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; } - gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); if (hiddenRows) { - drawMarker(i, starty, ypos); + drawMarker(g, av, i, starty, ypos); } } @@ -199,7 +196,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI gg.translate(0, transY); - drawIds(ss, es); + drawIds(gg, av, ss, es, searchResults); gg.translate(0, -transY); @@ -255,37 +252,43 @@ public class IdCanvas extends JPanel implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq()); + drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults); g.drawImage(image, 0, 0, this); } /** - * DOCUMENT ME! + * Draws sequence ids from sequence index starty to endy (inclusive), with the + * font and other display settings configured on the viewport. Ids of + * sequences included in the selection are coloured grey, otherwise the + * current id colour for the sequence id is used. * + * @param g + * @param alignViewport * @param starty - * DOCUMENT ME! * @param endy - * DOCUMENT ME! + * @param selection */ - void drawIds(int starty, int endy) + void drawIds(Graphics2D g, AlignViewport alignViewport, final int starty, + final int endy, List selection) { - if (av.isSeqNameItalics()) + Font font = alignViewport.getFont(); + if (alignViewport.isSeqNameItalics()) { - setIdfont(new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize())); + setIdfont(new Font(font.getName(), Font.ITALIC, + font.getSize())); } else { - setIdfont(av.getFont()); + setIdfont(font); } - gg.setFont(getIdfont()); - fm = gg.getFontMetrics(); + g.setFont(getIdfont()); + FontMetrics fm = g.getFontMetrics(); - if (av.antiAlias) + if (alignViewport.antiAlias) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } @@ -294,37 +297,33 @@ public class IdCanvas extends JPanel implements ViewportListenerI boolean hasHiddenRows = av.hasHiddenRows(); - if (av.getWrapAlignment()) + if (alignViewport.getWrapAlignment()) { drawIdsWrapped(starty, hasHiddenRows); return; } - // 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.getAlignment().getSequenceAt(i); + SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); if (sequence == null) { continue; } - if (hasHiddenRows || av.isDisplayReferenceSeq()) + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) { - setHiddenFont(sequence); + g.setFont(getHiddenFont(sequence, alignViewport)); } // Selected sequence colours - if ((searchResults != null) && searchResults.contains(sequence)) + if (selection != null && selection.contains(sequence)) { currentColor = Color.black; currentTextColor = Color.white; @@ -337,31 +336,32 @@ public class IdCanvas extends JPanel implements ViewportListenerI } else { - currentColor = av.getSequenceColour(sequence); + currentColor = alignViewport.getSequenceColour(sequence); currentTextColor = Color.black; } - gg.setColor(currentColor); + g.setColor(currentColor); - gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(), - av.getCharHeight()); + int charHeight = alignViewport.getCharHeight(); + g.fillRect(0, (i - starty) * charHeight, + getWidth(), charHeight); - gg.setColor(currentTextColor); + g.setColor(currentTextColor); - String string = sequence.getDisplayId(av.getShowJVSuffix()); + String string = sequence + .getDisplayId(alignViewport.getShowJVSuffix()); - if (av.isRightAlignIds()) + if (alignViewport.isRightAlignIds()) { xPos = panelWidth - fm.stringWidth(string) - 4; } - gg.drawString(string, xPos, - (((i - starty) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + g.drawString(string, xPos, (((i - starty) * charHeight) + charHeight) + - (charHeight / 5)); if (hasHiddenRows) { - drawMarker(i, starty, 0); + drawMarker(g, alignViewport, i, starty, 0); } } } @@ -385,6 +385,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI int annotationHeight = 0; + AnnotationLabels labels = null; if (av.isShowAnnotation()) { if (ap == null) @@ -393,10 +394,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI } annotationHeight = ap.adjustPanelHeight(); - if (labels == null) - { - labels = new AnnotationLabels(av); - } + labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -424,7 +422,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI SequenceI s = av.getAlignment().getSequenceAt(i); if (hasHiddenRows || av.isDisplayReferenceSeq()) { - setHiddenFont(s); + gg.setFont(getHiddenFont(s, av)); } else { @@ -446,18 +444,27 @@ public class IdCanvas extends JPanel implements ViewportListenerI } } - void drawMarker(int i, int starty, int yoffset) + /** + * Draws a marker (a blue right-pointing triangle) between sequences to + * indicate hidden sequences. + * + * @param g + * @param alignViewport + * @param seqIndex + * @param starty + * @param yoffset + */ + void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset) { - - SequenceI[] hseqs = av.getAlignment() + SequenceI[] hseqs = alignViewport.getAlignment() .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; + int hiddenIndex = seqIndex; + int lastIndex = seqIndex - 1; + int nextIndex = seqIndex + 1; for (int j = 0; j < hSize; j++) { @@ -478,52 +485,56 @@ public class IdCanvas extends JPanel implements ViewportListenerI } } + /* + * are we below or above the hidden sequences? + */ boolean below = (hiddenIndex > lastIndex + 1); boolean above = (nextIndex > hiddenIndex + 1); - gg.setColor(Color.blue); + g.setColor(Color.blue); + int charHeight = av.getCharHeight(); + + /* + * vertices of the triangle, below or above hidden seqs + */ + int[] xPoints = new int[] + { getWidth() - charHeight, + getWidth() - charHeight, getWidth() }; + int yShift = seqIndex - starty; + if (below) { - gg.fillPolygon( - new int[] - { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] - { (i - starty) * av.getCharHeight() + yoffset, - (i - starty) * av.getCharHeight() + yoffset - + av.getCharHeight() / 4, - (i - starty) * av.getCharHeight() + yoffset }, - 3); + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset + charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } if (above) { - gg.fillPolygon( - new int[] - { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] - { (i - starty + 1) * av.getCharHeight() + yoffset, - (i - starty + 1) * av.getCharHeight() + yoffset - - av.getCharHeight() / 4, - (i - starty + 1) * av.getCharHeight() + yoffset }, - 3); - + yShift++; + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset - charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } } - void setHiddenFont(SequenceI seq) + /** + * Answers the standard sequence id font, or a bold font if the sequence is + * set as reference or a hidden group representative + * + * @param seq + * @param alignViewport + * @return + */ + private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport) { - Font bold = new Font(av.getFont().getName(), Font.BOLD, - av.getFont().getSize()); - if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) { - gg.setFont(bold); - } - else - { - gg.setFont(getIdfont()); + return new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); } + return getIdfont(); } /**