-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class IdCanvas\r
- extends Panel\r
-{\r
- protected AlignViewport av;\r
-\r
- protected boolean showScores = true;\r
-\r
- protected int maxIdLength = -1;\r
- protected String maxIdStr = null;\r
- Image image;\r
- Graphics gg;\r
- int imgHeight = 0;\r
- boolean fastPaint = false;\r
-\r
- java.util.Vector searchResults;\r
-\r
- public IdCanvas(AlignViewport av)\r
- {\r
- setLayout(null);\r
- this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
- }\r
-\r
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,\r
- int ypos)\r
- {\r
- int charHeight = av.getCharHeight();\r
-\r
- if (searchResults != null && searchResults.contains(s))\r
- {\r
- gg.setColor(Color.black);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
- getSize().width, charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else if (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().getSequences(false).contains(s))\r
- {\r
- gg.setColor(Color.lightGray);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
- getSize().width, charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else\r
- {\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
- getSize().width, charHeight);\r
- gg.setColor(Color.black);\r
- }\r
-\r
-\r
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,\r
- ((i - starty) * charHeight) + ypos +\r
- charHeight - (charHeight / 5));\r
-\r
- if (av.hasHiddenRows && av.showHiddenMarkers)\r
- drawMarker(i, starty, ypos);\r
-\r
- }\r
-\r
- public void fastPaint(int vertical)\r
- {\r
- if (gg == null)\r
- {\r
- repaint();\r
- return;\r
- }\r
-\r
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);\r
-\r
- int ss = av.startSeq, es = av.endSeq, transY = 0;\r
- if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
- {\r
- ss = av.startSeq;\r
- }\r
- else\r
- {\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if (es > av.endSeq)\r
- {\r
- es = av.endSeq;\r
- }\r
- }\r
-\r
- gg.translate(0, transY);\r
-\r
- drawIds(ss, es);\r
-\r
- gg.translate(0, -transY);\r
-\r
- fastPaint = true;\r
- repaint();\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- if (getSize().height < 0 || getSize().width < 0)\r
- {\r
- return;\r
- }\r
- if (fastPaint)\r
- {\r
- fastPaint = false;\r
- g.drawImage(image, 0, 0, this);\r
- return;\r
- }\r
-\r
- imgHeight = getSize().height;\r
- imgHeight -= imgHeight % av.charHeight;\r
-\r
- if (imgHeight < 1)\r
- {\r
- return;\r
- }\r
-\r
- if (image == null || imgHeight != image.getHeight(this))\r
- {\r
- image = createImage(getSize().width, imgHeight);\r
- gg = image.getGraphics();\r
- gg.setFont(av.getFont());\r
- }\r
-\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- gg.setFont(italic);\r
-\r
- gg.fillRect(0, 0, getSize().width, getSize().height);\r
- drawIds(av.startSeq, av.endSeq);\r
- g.drawImage(image, 0, 0, this);\r
- }\r
-\r
- void drawIds(int starty, int endy)\r
- {\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
-\r
- gg.setFont(italic);\r
-\r
- Color currentColor = Color.white;\r
- Color currentTextColor = Color.black;\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int maxwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\r
-\r
- if (av.hasHiddenColumns)\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
-\r
- int annotationHeight = 0;\r
- AnnotationLabels labels = null;\r
-\r
- if (av.showAnnotation)\r
- {\r
- AnnotationPanel ap = new AnnotationPanel(av);\r
- annotationHeight = ap.adjustPanelHeight();\r
- labels = new AnnotationLabels(av);\r
- }\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int cHeight = alheight * av.charHeight\r
- + hgap\r
- + annotationHeight;\r
-\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
-\r
- // Draw the rest of the panels\r
- for (int ypos = hgap, row = av.startRes;\r
- (ypos <= getSize().height) && (row < maxwidth);\r
- ypos += cHeight, row += rowSize)\r
- {\r
- for (int i = starty; i < alheight; i++)\r
- {\r
- if (av.hasHiddenRows)\r
- {\r
- setHiddenFont(i);\r
- }\r
- else\r
- gg.setFont(italic);\r
-\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
-\r
- if (labels != null)\r
- {\r
- gg.translate(0, ypos + (alheight * av.charHeight));\r
- labels.drawComponent(gg, getSize().width);\r
- gg.translate(0, -ypos - (alheight * av.charHeight));\r
- }\r
-\r
- }\r
- }\r
- else\r
- {\r
- //Now draw the id strings\r
-\r
- //Now draw the id strings\r
- for (int i = starty; i < endy; i++)\r
- {\r
- if (av.hasHiddenRows)\r
- {\r
- setHiddenFont(i);\r
- }\r
-\r
- // Selected sequence colours\r
- if ( (searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- currentColor = Color.black;\r
- currentTextColor = Color.white;\r
- }\r
- else if ( (av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().getSequences(false).contains(\r
- av.alignment.getSequenceAt(i)))\r
- {\r
- currentColor = Color.lightGray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
-\r
- gg.setColor(currentColor);\r
-\r
- gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,\r
- av.charHeight);\r
-\r
- gg.setColor(currentTextColor);\r
-\r
- String string = av.alignment.getSequenceAt(i).getDisplayId(av.\r
- getShowJVSuffix());\r
-\r
- gg.drawString(string, 0,\r
- ( ( (i - starty) * av.charHeight) + av.charHeight) -\r
- (av.charHeight / 5));\r
-\r
- if (av.hasHiddenRows && av.showHiddenMarkers)\r
- drawMarker(i, starty, 0);\r
- }\r
- }\r
- }\r
-\r
- public void setHighlighted(java.util.Vector found)\r
- {\r
- searchResults = found;\r
- repaint();\r
- }\r
-\r
- void drawMarker(int i, int starty, int yoffset)\r
- {\r
- SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
- //Use this method here instead of calling hiddenSeq adjust\r
- //3 times.\r
- int hSize = hseqs.length;\r
-\r
- int hiddenIndex = i;\r
- int lastIndex = i - 1;\r
- int nextIndex = i + 1;\r
-\r
- boolean below = (hiddenIndex > lastIndex + 1);\r
- boolean above = (nextIndex > hiddenIndex + 1);\r
-\r
-\r
-\r
- for(int j=0; j<hSize; j++)\r
- {\r
- if (hseqs[j] != null)\r
- {\r
- if(j-1<hiddenIndex)\r
- hiddenIndex++;\r
- if(j-1<lastIndex)\r
- lastIndex++;\r
- if(j-1<nextIndex)\r
- nextIndex++;\r
- }\r
- }\r
-\r
- gg.setColor(Color.blue);\r
- if(below)\r
- {\r
- gg.fillPolygon(new int[]\r
- {getSize().width- av.charHeight,\r
- getSize().width- av.charHeight,\r
- getSize().width},\r
- new int[]\r
- {\r
- (i - starty) * av.charHeight +yoffset,\r
- (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,\r
- (i - starty) * av.charHeight+yoffset\r
- }, 3);\r
- }\r
- if(above)\r
- {\r
- gg.fillPolygon(new int[]\r
- {getSize().width- av.charHeight,\r
- getSize().width - av.charHeight,\r
- getSize().width },\r
- new int[]\r
- {\r
- (i - starty+1) * av.charHeight +yoffset,\r
- (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,\r
- (i - starty+1) * av.charHeight +yoffset\r
- }, 3);\r
-\r
- }\r
- }\r
-\r
- void setHiddenFont(int i)\r
- {\r
- /* System.out.println(i+" "+av.alignment.getHeight());\r
- if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
- gg.setFont(new Font(av.getFont().getName(), Font.BOLD,\r
- av.getFont().getSize()));\r
- else\r
- gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize()));*/\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<SequenceI> 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<SequenceI> 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff