X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=58a4f107519548f27d3e5398983a05484f67f677;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=f7f1b203b5f237c149edfcad4bb7dc4e677b2693;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index f7f1b20..58a4f10 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,276 +1,388 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class IdCanvas
- extends Panel
-{
- protected AlignViewport av;
-
- protected boolean showScores = true;
-
- protected int maxIdLength = -1;
- protected String maxIdStr = null;
- Image image;
- Graphics gg;
- int imgHeight = 0;
- boolean fastPaint = false;
-
- java.util.Vector searchResults;
-
- public IdCanvas(AlignViewport av)
- {
- setLayout(null);
- this.av = av;
- PaintRefresher.Register(this, av.alignment);
- }
-
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
- int ypos)
- {
- int charHeight = av.getCharHeight();
-
- if (searchResults != null && searchResults.contains(s))
- {
- gg.setColor(Color.black);
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
- gg.setColor(Color.white);
- }
- else if (av.getSelectionGroup() != null &&
- av.getSelectionGroup().getSequences(false).contains(s))
- {
- gg.setColor(Color.lightGray);
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
- gg.setColor(Color.white);
- }
- else
- {
- gg.setColor(s.getColor());
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
- gg.setColor(Color.black);
- }
-
-
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,
- ((i - starty) * charHeight) + ypos +
- charHeight - (charHeight / 5));
-
- }
-
- public void fastPaint(int vertical)
- {
- if (gg == null)
- {
- repaint();
- return;
- }
-
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
-
- int ss = av.startSeq, es = av.endSeq, transY = 0;
- if (vertical > 0) // scroll down
- {
- ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
- {
- ss = av.startSeq;
- }
- else
- {
- transY = imgHeight - vertical * av.charHeight;
- }
- }
- else if (vertical < 0)
- {
- es = ss - vertical;
- if (es > av.endSeq)
- {
- es = av.endSeq;
- }
- }
-
- gg.translate(0, transY);
-
- drawIds(ss, es);
-
- gg.translate(0, -transY);
-
- fastPaint = true;
- repaint();
- }
-
- public void update(Graphics g)
- {
- paint(g);
- }
-
- public void paint(Graphics g)
- {
- if (getSize().height < 0 || getSize().width < 0)
- {
- return;
- }
- if (fastPaint)
- {
- fastPaint = false;
- g.drawImage(image, 0, 0, this);
- return;
- }
-
- imgHeight = getSize().height;
- imgHeight -= imgHeight % av.charHeight;
-
- if (imgHeight < 1)
- {
- return;
- }
-
- if (image == null || imgHeight != image.getHeight(this))
- {
- image = createImage(getSize().width, imgHeight);
- gg = image.getGraphics();
- gg.setFont(av.getFont());
- }
-
- //Fill in the background
- gg.setColor(Color.white);
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
- gg.setFont(italic);
-
- gg.fillRect(0, 0, getSize().width, getSize().height);
- drawIds(av.getStartSeq(), av.endSeq);
- g.drawImage(image, 0, 0, this);
- }
-
- void drawIds(int starty, int endy)
- {
- Color currentColor = Color.white;
- Color currentTextColor = Color.black;
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
-
- if (av.getWrapAlignment())
- {
- int annotationHeight = 0;
- AnnotationLabels labels = null;
-
- if(av.showAnnotation)
- {
- AnnotationPanel ap = new AnnotationPanel(av);
- annotationHeight = ap.adjustPanelHeight();
- labels = new AnnotationLabels(av);
- }
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
-
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap
- + annotationHeight;
-
- int rowSize = av.getEndRes() - av.getStartRes();
-
- // Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes;
- (ypos <= getSize().height) && (row < av.alignment.getWidth());
- ypos += cHeight, row += rowSize)
- {
- for (int i = starty; i < av.alignment.getHeight(); i++)
- {
- SequenceI s = av.alignment.getSequenceAt(i);
- gg.setFont(italic);
- drawIdString(gg, s, i, 0, ypos);
- }
-
- if(labels!=null)
- {
- gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));
- labels.drawComponent(gg, getSize().width);
- gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));
- }
- }
-
- }
- else
- {
-
- //Now draw the id strings
- for (int i = starty; i < endy; i++)
- {
- // Selected sequence colours
-
- if (searchResults != null &&
- searchResults.contains(av.alignment.getSequenceAt(i)))
- {
- gg.setColor(Color.black);
- currentColor = Color.black;
- currentTextColor = Color.white;
- }
- else if (av.getSelectionGroup() != null
- &&
- av.getSelectionGroup().getSequences(false).contains(av.alignment.
- getSequenceAt(i)))
- {
- currentColor = Color.lightGray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.alignment.getSequenceAt(i).getColor();
- currentTextColor = Color.black;
- }
-
- gg.setColor(currentColor);
-
- gg.fillRect(0,
- ((i - starty) * av.charHeight),
- getSize().width,
- av.charHeight);
-
- gg.setColor(currentTextColor);
-
- gg.drawString(av.alignment.getSequenceAt(i)
- .getDisplayId(av.getShowJVSuffix()), 0,
- ((i - starty) * av.charHeight) +
- av.charHeight - (av.charHeight / 5));
- }
-
- // add a border
- gg.setColor(Color.white);
- gg.fillRect(getSize().width - 4, 0, 4, getSize().height);
- }
-
- }
-
- public void setHighlighted(java.util.Vector found)
- {
- searchResults = found;
- repaint();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
+
+public class IdCanvas extends Panel
+{
+ protected AlignViewport av;
+
+ protected boolean showScores = true;
+
+ protected int maxIdLength = -1;
+
+ protected String maxIdStr = null;
+
+ Image image;
+
+ Graphics gg;
+
+ int imgHeight = 0;
+
+ boolean fastPaint = false;
+
+ List searchResults;
+
+ public IdCanvas(AlignViewport av)
+ {
+ setLayout(null);
+ this.av = av;
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ }
+
+ public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
+ {
+ int charHeight = av.getCharHeight();
+
+ if (searchResults != null && searchResults.contains(s))
+ {
+ gg.setColor(Color.black);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+ charHeight);
+ gg.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, getSize().width,
+ charHeight);
+ gg.setColor(Color.white);
+ }
+ else
+ {
+ gg.setColor(av.getSequenceColour(s));
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+ charHeight);
+ gg.setColor(Color.black);
+ }
+
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+ ((i - starty) * charHeight) + ypos + charHeight
+ - (charHeight / 5));
+
+ if (hiddenRows)
+ {
+ drawMarker(i, starty, ypos);
+ }
+
+ }
+
+ public void fastPaint(int vertical)
+ {
+ if (gg == null)
+ {
+ repaint();
+ return;
+ }
+
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+ -vertical * av.getCharHeight());
+
+ int ss = av.startSeq, es = av.endSeq, transY = 0;
+ if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ {
+ ss = av.startSeq;
+ }
+ else
+ {
+ transY = imgHeight - vertical * av.getCharHeight();
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(0, transY);
+
+ drawIds(ss, es);
+
+ gg.translate(0, -transY);
+
+ fastPaint = true;
+ repaint();
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+ if (getSize().height < 0 || getSize().width < 0)
+ {
+ return;
+ }
+ if (fastPaint)
+ {
+ fastPaint = false;
+ g.drawImage(image, 0, 0, this);
+ return;
+ }
+
+ imgHeight = getSize().height;
+ imgHeight -= imgHeight % av.getCharHeight();
+
+ if (imgHeight < 1)
+ {
+ return;
+ }
+
+ if (image == null || imgHeight != image.getHeight(this))
+ {
+ image = createImage(getSize().width, imgHeight);
+ gg = image.getGraphics();
+ gg.setFont(av.getFont());
+ }
+
+ // Fill in the background
+ gg.setColor(Color.white);
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
+ gg.setFont(italic);
+
+ gg.fillRect(0, 0, getSize().width, getSize().height);
+ drawIds(av.startSeq, av.endSeq);
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * local copy of av.getCharHeight set at top of drawIds
+ */
+ private int avcharHeight;
+
+ void drawIds(int starty, int endy)
+ {
+ // hardwired italic IDs in applet currently
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
+ // temp variable for speed
+ avcharHeight = av.getCharHeight();
+
+ gg.setFont(italic);
+
+ Color currentColor = Color.white;
+ Color currentTextColor = Color.black;
+
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+ && av.getShowHiddenMarkers();
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+
+ if (av.isShowAnnotation())
+ {
+ AnnotationPanel ap = new AnnotationPanel(av);
+ annotationHeight = ap.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += avcharHeight;
+ }
+
+ int cHeight = alheight * avcharHeight + hgap + annotationHeight;
+
+ int rowSize = av.getEndRes() - av.getStartRes();
+ // Draw the rest of the panels
+ for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+ && (row < maxwidth); ypos += cHeight, row += rowSize)
+ {
+ for (int i = starty; i < alheight; i++)
+ {
+
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ gg.setFont(italic);
+ if (doHiddenCheck)
+ {
+ setHiddenFont(s);
+ }
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
+ }
+
+ if (labels != null)
+ {
+ gg.translate(0, ypos + (alheight * avcharHeight));
+ labels.drawComponent(gg, getSize().width);
+ gg.translate(0, -ypos - (alheight * avcharHeight));
+ }
+
+ }
+ }
+ else
+ {
+ // Now draw the id strings
+ SequenceI seq;
+ for (int i = starty; i < endy; i++)
+ {
+
+ seq = av.getAlignment().getSequenceAt(i);
+ if (seq == null)
+ {
+ continue;
+ }
+ gg.setFont(italic);
+ // boolean isrep=false;
+ if (doHiddenCheck)
+ {
+ // isrep =
+ setHiddenFont(seq);
+ }
+
+ // Selected sequence colours
+ if ((searchResults != null) && searchResults.contains(seq))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
+ }
+
+ gg.setColor(currentColor);
+ // TODO: isrep could be used to highlight the representative in a
+ // different way
+ gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+ avcharHeight);
+ gg.setColor(currentTextColor);
+
+ gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
+ (((i - starty) * avcharHeight) + avcharHeight)
+ - (avcharHeight / 5));
+
+ if (hiddenRows)
+ {
+ drawMarker(i, starty, 0);
+ }
+ }
+ }
+ }
+
+ public void setHighlighted(List list)
+ {
+ searchResults = list;
+ repaint();
+ }
+
+ void drawMarker(int i, int starty, int yoffset)
+ {
+ SequenceI[] hseqs = av.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;
+
+ 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[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty) * avcharHeight + yoffset,
+ (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+ (i - starty) * avcharHeight + yoffset }, 3);
+ }
+ if (above)
+ {
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty + 1) * avcharHeight + yoffset,
+ (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+ (i - starty + 1) * avcharHeight + yoffset }, 3);
+
+ }
+ }
+
+ boolean setHiddenFont(SequenceI seq)
+ {
+ Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+ .getSize());
+
+ if (av.isHiddenRepSequence(seq))
+ {
+ gg.setFont(bold);
+ return true;
+ }
+ return false;
+ }
+}