/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\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
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
*/\r
-\r
package jalview.appletgui;\r
\r
-import java.awt.*;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
\r
-import jalview.datamodel.*;\r
+import java.awt.Color;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+import java.awt.Image;\r
+import java.awt.Panel;\r
\r
-public class SeqCanvas\r
- extends Panel\r
+public class SeqCanvas extends Panel\r
{\r
FeatureRenderer fr;\r
+\r
SequenceRenderer sr;\r
+\r
Image img;\r
+\r
Graphics gg;\r
+\r
int imgWidth;\r
+\r
int imgHeight;\r
\r
AlignViewport av;\r
\r
- boolean displaySearch = false;\r
- int[] searchResults = null;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
+ SearchResults searchResults = null;\r
\r
boolean fastPaint = false;\r
\r
+ int cursorX = 0;\r
+\r
+ int cursorY = 0;\r
\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
fr = new FeatureRenderer(av);\r
sr = new SequenceRenderer(av);\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public AlignViewport getViewport()\r
return fr;\r
}\r
\r
- MCview.AppletPDBCanvas pdbCanvas;\r
public SequenceRenderer getSequenceRenderer()\r
{\r
return sr;\r
}\r
\r
- public void setPDBCanvas(MCview.AppletPDBCanvas pc)\r
- {\r
- pdbCanvas = pc;\r
- }\r
-\r
-\r
void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
{\r
int scalestartx = startx - startx % 10 + 10;\r
// NORTH SCALE\r
for (int i = scalestartx; i < endx; i += 10)\r
{\r
- String string = String.valueOf(i);\r
- g.drawString(string, (i - startx - 1) * av.charWidth,\r
- ypos - av.charHeight / 2);\r
+ int value = i;\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+ }\r
\r
- g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,\r
- ypos + 2 - av.charHeight / 2,\r
- (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);\r
+ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
+ ypos - (av.charHeight / 2));\r
\r
+ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ (ypos + 2) - (av.charHeight / 2),\r
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ ypos - 2);\r
}\r
}\r
\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
ypos += av.charHeight;\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ if (av.hasHiddenColumns())\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ int maxwidth = av.getAlignment().getWidth();\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ // WEST SCALE\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.getAlignment().getSequenceAt(i);\r
int index = startx;\r
int value = -1;\r
+\r
while (index < endx)\r
{\r
if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
{\r
index++;\r
+\r
continue;\r
}\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);\r
+\r
break;\r
}\r
+\r
if (value != -1)\r
{\r
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
- g.drawString(value + "", x,\r
- ypos + i * av.charHeight - av.charHeight / 5);\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))\r
+ - av.charWidth / 2;\r
+ g.drawString(value + "", x, (ypos + (i * av.charHeight))\r
+ - (av.charHeight / 5));\r
}\r
}\r
}\r
void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
{\r
ypos += av.charHeight;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ SequenceI seq;\r
// EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
+ seq = av.getAlignment().getSequenceAt(i);\r
int index = endx;\r
int value = -1;\r
+\r
while (index > startx)\r
{\r
if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
{\r
index--;\r
+\r
continue;\r
}\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ value = seq.findPosition(index);\r
+\r
break;\r
}\r
+\r
if (value != -1)\r
{\r
- g.drawString(value + "", av.charWidth/2,\r
- ypos + i * av.charHeight - av.charHeight / 5);\r
+ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))\r
+ - (av.charHeight / 5));\r
}\r
}\r
-\r
}\r
\r
- public void fastPaint(int horizontal, int vertical)\r
+ int lastsr = 0;\r
+\r
+ void fastPaint(int horizontal, int vertical)\r
{\r
- if (gg == null)\r
+ if (fastPaint || gg == null)\r
{\r
return;\r
}\r
\r
- gg.copyArea(horizontal * av.charWidth,\r
- vertical * av.charHeight,\r
- imgWidth,\r
- imgHeight,\r
- -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ // Its possible on certain browsers that the call to fastpaint\r
+ // is faster than it can paint, so this check here catches\r
+ // this possibility\r
+ if (lastsr + horizontal != av.startRes)\r
+ {\r
+ horizontal = av.startRes - lastsr;\r
+ }\r
+\r
+ lastsr = av.startRes;\r
+\r
+ fastPaint = true;\r
+ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,\r
+ imgWidth - horizontal * av.charWidth, imgHeight - vertical\r
+ * av.charHeight, -horizontal * av.charWidth, -vertical\r
+ * av.charHeight);\r
+\r
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;\r
\r
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
- transX = 0, transY = 0;\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
transX = (er - sr - horizontal) * av.charWidth;\r
\r
gg.translate(transX, transY);\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);\r
- drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
- gg.translate( -transX, -transY);\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
+ gg.translate(-transX, -transY);\r
\r
- fastPaint = true;\r
repaint();\r
\r
}\r
\r
/**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\r
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working\r
+ * towards! startx is the first residue (starting at 0) to display. endx is\r
+ * the last residue to display (starting at 0). starty is the first sequence\r
+ * to display (starting at 0). endy is the last sequence to display (starting\r
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the\r
+ * adjustment listener in SeqPanel when the scrollbars move.\r
*/\r
public void update(Graphics g)\r
{\r
\r
public void paint(Graphics g)\r
{\r
- sr.renderGaps(av.renderGaps);\r
+\r
+ if (img != null\r
+ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g\r
+ .getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
\r
if (fastPaint)\r
{\r
return;\r
}\r
\r
- if (img == null || imgWidth != img.getWidth(this) ||\r
- imgHeight != img.getHeight(this))\r
+ if (img == null || imgWidth != img.getWidth(this)\r
+ || imgHeight != img.getHeight(this))\r
{\r
img = createImage(imgWidth, imgHeight);\r
gg = img.getGraphics();\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
-\r
if (av.getWrapAlignment())\r
{\r
drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
}\r
else\r
{\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,\r
- av.startSeq, 0);\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
\r
- if (pdbCanvas != null)\r
- {\r
- pdbCanvas.updateSeqColours();\r
- }\r
}\r
\r
int LABEL_WEST, LABEL_EAST;\r
+\r
public int getWrappedCanvasWidth(int cwidth)\r
{\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ cwidth -= cwidth % av.charWidth;\r
\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(getMask());\r
- }\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(getMask());\r
- }\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
\r
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- }\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ }\r
\r
/**\r
* Generates a string of zeroes.\r
+ * \r
* @return String\r
*/\r
String getMask()\r
{\r
- String mask = "00";\r
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+ String mask = "0";\r
+ int maxWidth = 0;\r
+ int tmp;\r
+ AlignmentI alignment = av.getAlignment();\r
+ for (int i = 0; i < alignment.getHeight(); i++)\r
+ {\r
+ tmp = alignment.getSequenceAt(i).getEnd();\r
+ if (tmp > maxWidth)\r
+ {\r
+ maxWidth = tmp;\r
+ }\r
+ }\r
+\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
{\r
mask += "0";\r
}\r
return mask;\r
- }\r
+ }\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
- int startRes)\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth,\r
+ int canvasHeight, int startRes)\r
{\r
AlignmentI al = av.getAlignment();\r
\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- int LABEL_EAST = 0;\r
-\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(getMask());\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
- int LABEL_WEST = 0;\r
-\r
if (av.scaleLeftWrapped)\r
{\r
- LABEL_WEST = fm.stringWidth(getMask());\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
int hgap = av.charHeight;\r
- if(av.scaleAboveWrapped)\r
+ if (av.scaleAboveWrapped)\r
+ {\r
hgap += av.charHeight;\r
+ }\r
\r
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
\r
av.endRes = av.startRes + cWidth;\r
\r
-\r
- int endx = (startRes + cWidth) - 1;\r
+ int endx;\r
int ypos = hgap;\r
\r
+ int maxwidth = av.getAlignment().getWidth() - 1;\r
\r
- while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ if (av.hasHiddenColumns())\r
{\r
- g.setColor(Color.black);\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- drawWestScale(g, startRes, endx, ypos);\r
- }\r
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
+ {\r
+ endx = startRes + cWidth - 1;\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate(-(canvasWidth - LABEL_EAST), 0);\r
- }\r
+ if (endx > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
\r
- g.translate(LABEL_WEST, 0);\r
+ g.setColor(Color.black);\r
\r
- if (av.scaleAboveWrapped)\r
- {\r
- drawNorthScale(g, startRes, endx, ypos);\r
- }\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
+ }\r
\r
+ g.translate(LABEL_WEST, 0);\r
\r
- if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)\r
+ {\r
+ g.setColor(Color.blue);\r
+ int res;\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
{\r
- endx = av.vconsensus.size() - 2;\r
- }\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i)\r
+ - startRes;\r
\r
+ if (res < 0 || res > endx - startRes)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ gg.fillPolygon(new int[]\r
+ { res * av.charWidth - av.charHeight / 4,\r
+ res * av.charWidth + av.charHeight / 4, res * av.charWidth },\r
+ new int[]\r
+ { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2) + 8 }, 3);\r
\r
- if(g.getClip()==null)\r
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
+ }\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(null);\r
+ if (g.getClip() == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+ g.setClip(null);\r
\r
- if(av.showAnnotation)\r
+ if (av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 4);\r
+ if (annotations == null)\r
{\r
- g.translate(0, cHeight + ypos+4);\r
- if(annotations==null)\r
- annotations = new AnnotationPanel(av);\r
-\r
- annotations.drawComponent( g, startRes, endx + 1);\r
- g.translate(0, -cHeight - ypos-4);\r
+ annotations = new AnnotationPanel(av);\r
}\r
- g.translate(-LABEL_WEST, 0);\r
-\r
- ypos += cHeight+getAnnotationHeight()+hgap;\r
\r
+ annotations.drawComponent(g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos - 4);\r
+ }\r
+ g.translate(-LABEL_WEST, 0);\r
\r
- startRes += cWidth;\r
- endx = (startRes + cWidth) - 1;\r
+ ypos += cHeight + getAnnotationHeight() + hgap;\r
\r
- if (endx > al.getWidth())\r
- {\r
- endx = al.getWidth();\r
- }\r
- }\r
+ startRes += cWidth;\r
+ }\r
\r
}\r
\r
AnnotationPanel annotations;\r
+\r
int getAnnotationHeight()\r
{\r
- if(!av.showAnnotation)\r
+ if (!av.showAnnotation)\r
+ {\r
return 0;\r
+ }\r
\r
- if(annotations==null)\r
+ if (annotations == null)\r
+ {\r
annotations = new AnnotationPanel(av);\r
+ }\r
\r
return annotations.adjustPanelHeight();\r
- }\r
+ }\r
\r
- synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,\r
- int startx, int starty, int offset)\r
+ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,\r
+ int endSeq, int offset)\r
{\r
\r
+\r
+ if (!av.hasHiddenColumns())\r
+ {\r
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+ else\r
+ {\r
+\r
+ int screenY = 0;\r
+ int blockStart = startRes;\r
+ int blockEnd = endRes;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ for (int[] region : av.getColumnSelection().getHiddenColumns())\r
+ {\r
+ int hideStart = region[0];\r
+ int hideEnd = region[1];\r
+\r
+ if (hideStart <= blockStart)\r
+ {\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
+\r
+ blockEnd = hideStart - 1;\r
+\r
+ g1.translate(screenY * av.charWidth, 0);\r
+\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ if (av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\r
+ g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ 0 + offset, (blockEnd - blockStart + 1) * av.charWidth\r
+ - 1, (endSeq - startSeq) * av.charHeight\r
+ + offset);\r
+ }\r
+\r
+ g1.translate(-screenY * av.charWidth, 0);\r
+ screenY += blockEnd - blockStart + 1;\r
+ blockStart = hideEnd + 1;\r
+ }\r
+ }\r
+ if (screenY <= (endRes - startRes))\r
+ {\r
+ blockEnd = blockStart + (endRes - startRes) - screenY;\r
+ g1.translate(screenY * av.charWidth, 0);\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ g1.translate(-screenY * av.charWidth, 0);\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
+ // int x1, int x2, int y1, int y2, int startx, int starty,\r
+ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,\r
+ int offset)\r
+ {\r
g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
+ sr.prepare(g, av.renderGaps);\r
\r
SequenceI nextSeq;\r
- /// First draw the sequences\r
- /////////////////////////////\r
- for (int i = y1; i < y2; i++)\r
- {\r
- nextSeq = av.alignment.getSequenceAt(i);\r
\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- (i - starty) * av.charHeight,\r
- av.charWidth, av.charHeight);\r
+ // / First draw the sequences\r
+ // ///////////////////////////\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ nextSeq = av.getAlignment().getSequenceAt(i);\r
+\r
+ if (nextSeq == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),\r
+ startRes, endRes, offset + ((i - startSeq) * av.charHeight));\r
+\r
+ if (av.isShowSequenceFeatures())\r
+ {\r
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+\r
+ // / Highlight search Results once all sequences have been drawn\r
+ // ////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
+ endRes);\r
+ if (visibleResults != null)\r
+ {\r
+ for (int r = 0; r < visibleResults.length; r += 2)\r
+ {\r
+ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
+ visibleResults[r + 1], (visibleResults[r] - startRes)\r
+ * av.charWidth, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.cursorMode && cursorY == i && cursorX >= startRes\r
+ && cursorX <= endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX,\r
+ (cursorX - startRes) * av.charWidth, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+ }\r
\r
- if (av.showSequenceFeatures)\r
+ if (av.getSelectionGroup() != null\r
+ || av.getAlignment().getGroups().size() > 0)\r
{\r
- fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- (i - starty) * av.charHeight,\r
- av.charWidth, av.charHeight);\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
}\r
- }\r
\r
- /////////////////////////////////////\r
+ }\r
\r
+ void drawGroupsBoundaries(Graphics g, int startRes, int endRes,\r
+ int startSeq, int endSeq, int offset)\r
+ {\r
+ //\r
+ // ///////////////////////////////////\r
// Now outline any areas if necessary\r
- /////////////////////////////////////\r
+ // ///////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
- int sx = -1, sy = -1, ex = -1;\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
int groupIndex = -1;\r
- if (group == null && groups.size() > 0)\r
+\r
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ group = av.getAlignment().getGroups().get(0);\r
groupIndex = 0;\r
}\r
+\r
if (group != null)\r
{\r
- do\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
+ int alHeight = av.getAlignment().getHeight() - 1;\r
+\r
+ for (i = startSeq; i < endSeq; i++)\r
{\r
- int oldY = -1;\r
- int i = 0;\r
- boolean inGroup = false;\r
- int top = -1;\r
- int bottom = -1;\r
+ sx = (group.getStartRes() - startRes) * av.charWidth;\r
+ sy = offset + ((i - startSeq) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;\r
+\r
+ if (sx + ex < 0 || sx > imgWidth)\r
+ {\r
+ continue;\r
+ }\r
\r
- for (i = y1; i < y2; i++)\r
+ if ((sx <= (endRes - startRes) * av.charWidth)\r
+ && group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ if ((bottom == -1)\r
+ && (i >= alHeight || !group.getSequences(null)\r
+ .contains(\r
+ av.getAlignment().getSequenceAt(i + 1))))\r
{\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + ((i - starty) * av.charHeight);\r
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
- 1;\r
-\r
- if(sx+ex<0 || sx>imgWidth)\r
- {\r
- continue;\r
- }\r
-\r
- if ( (sx <= (x2-x1)*av.charWidth) &&\r
- group.sequences.contains(av.alignment.getSequenceAt(\r
- i)))\r
- {\r
-\r
- if (bottom == -1)\r
- {\r
- if(i == y2-1 || // Dont check for i+1 if on the bottom row\r
- !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
-\r
- bottom = sy + av.charHeight;\r
- }\r
-\r
- if (!inGroup)\r
- {\r
- if (((top == -1) && (i == 0)) ||\r
- !group.sequences.contains(\r
- av.alignment.getSequenceAt(i - 1)))\r
- {\r
- top = sy;\r
- }\r
-\r
- oldY = sy;\r
- inGroup = true;\r
-\r
- if (group == av.getSelectionGroup())\r
- {\r
-\r
- g.setColor(Color.red);\r
- }\r
- else\r
- {\r
- g.setColor(group.getOutlineColour());\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (inGroup)\r
- {\r
- if (sx >= 0 && sx < imgWidth)\r
- g.drawLine(sx, oldY, sx, sy);\r
-\r
- if (sx + ex < imgWidth)\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
-\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
-\r
- if (sx + ex > imgWidth)\r
- ex = imgWidth;\r
-\r
- else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
- ex = (x2 - x1 + 1) * av.charWidth;\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
-\r
- inGroup = false;\r
- }\r
- }\r
+ bottom = sy + av.charHeight;\r
}\r
\r
+ if (!inGroup)\r
+ {\r
+ if (((top == -1) && (i == 0))\r
+ || !group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
if (inGroup)\r
{\r
- sy = offset + ( (i - starty) * av.charHeight);\r
if (sx >= 0 && sx < imgWidth)\r
+ {\r
g.drawLine(sx, oldY, sx, sy);\r
+ }\r
\r
if (sx + ex < imgWidth)\r
+ {\r
g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
\r
if (sx < 0)\r
{\r
}\r
\r
if (sx + ex > imgWidth)\r
+ {\r
ex = imgWidth;\r
- else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
- ex = (x2 - x1 + 1) * av.charWidth;\r
+ }\r
+\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
\r
if (top != -1)\r
{\r
\r
if (bottom != -1)\r
{\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
bottom = -1;\r
}\r
\r
- inGroup = false;\r
+ inGroup = false;\r
}\r
-\r
- groupIndex++;\r
-\r
- if (groupIndex >= groups.size())\r
- {\r
- break;\r
- }\r
-\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ }\r
}\r
- while (groupIndex < groups.size());\r
- }\r
\r
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if (displaySearch)\r
- {\r
- for (int r = 0; r < searchResults.length; r += 3)\r
- {\r
- int searchSeq = searchResults[r];\r
-\r
- if (searchSeq >= y1 && searchSeq < y2)\r
+ if (inGroup)\r
{\r
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
+ sy = offset + ((i - startSeq) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < imgWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
\r
- int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
- int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ {\r
+ ex = imgWidth;\r
+ }\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if (searchStart < x1)\r
+ if (top != -1)\r
{\r
- searchStart = x1;\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
}\r
- if (searchEnd > x2)\r
+\r
+ if (bottom != -1)\r
{\r
- searchEnd = x2;\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
}\r
\r
- ssr.drawHighlightedText(seq,\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- (searchSeq-starty)*av.charHeight,\r
- av.charWidth,\r
- av.charHeight);\r
+ inGroup = false;\r
}\r
- }\r
- }\r
\r
- }\r
+ groupIndex++;\r
+\r
+ if (groupIndex >= av.getAlignment().getGroups().size())\r
+ {\r
+ break;\r
+ }\r
+\r
+ group = av.getAlignment().getGroups()\r
+ .get(groupIndex);\r
+ } while (groupIndex < av.getAlignment().getGroups().size());\r
\r
- public void highlightSearchResults(int[] results)\r
- {\r
- // results are in the order sequence, startRes, endRes\r
- if (results == null)\r
- {\r
- displaySearch = false;\r
- }\r
- else\r
- {\r
- displaySearch = true;\r
}\r
+ }\r
\r
+ public void highlightSearchResults(SearchResults results)\r
+ {\r
searchResults = results;\r
\r
repaint();\r
git://source.jalview.org / jalview.git / blobdiff