/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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
+ * \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
* 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
/**\r
- * DOCUMENT ME!\r
+ * Column number at position i in selection\r
*\r
- * @param i DOCUMENT ME!\r
+ * @param i index into selected columns\r
*\r
- * @return DOCUMENT ME!\r
+ * @return column number in alignment\r
*/\r
public int columnAt(int i)\r
{\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * rightmost selected column\r
*\r
- * @return DOCUMENT ME!\r
+ * @return rightmost column in alignment that is selected\r
*/\r
public int getMax()\r
{\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Leftmost column in selection\r
*\r
- * @return DOCUMENT ME!\r
+ * @return column index of leftmost column in selection\r
*/\r
public int getMin()\r
{\r
}\r
\r
/**\r
- * THis method returns the rightmost limit of a\r
+ * This method returns the leftmost limit of a\r
* region of an alignment with hidden columns.\r
- * In otherwords, the next hidden column.\r
+ * In otherwords, the previous hidden column.\r
* @param index int\r
*/\r
public int getHiddenBoundaryLeft(int alPos)\r
\r
public boolean isVisible(int column)\r
{\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if (column >= region[0] && column <= region[1])\r
+ if (hiddenColumns != null)\r
+ for (int i = 0; i < hiddenColumns.size(); i++)\r
{\r
- return false;\r
+ int[] region = (int[]) hiddenColumns.elementAt(i);\r
+ if (column >= region[0] && column <= region[1])\r
+ {\r
+ return false;\r
+ }\r
}\r
- }\r
+\r
return true;\r
}\r
\r
start, end - 1};\r
}\r
}\r
+\r
+ /**\r
+ * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).\r
+ * @param alignmentAnnotation\r
+ */\r
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)\r
+ {\r
+ makeVisibleAnnotation(-1,-1,alignmentAnnotation);\r
+ }\r
+ /**\r
+ * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).\r
+ * @param start remove any annotation to the right of this column\r
+ * @param end remove any annotation to the left of this column\r
+ * @param alignmentAnnotation the annotation to operate on\r
+ */\r
+ public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)\r
+ {\r
+ if (alignmentAnnotation.annotations==null)\r
+ {\r
+ return;\r
+ }\r
+ if (start==end && end==-1)\r
+ {\r
+ start = 0;\r
+ end = alignmentAnnotation.annotations.length;\r
+ }\r
+ if (hiddenColumns != null && hiddenColumns.size() > 0)\r
+ {\r
+ // then mangle the alignmentAnnotation annotation array\r
+ Vector annels = new Vector();\r
+ Annotation[] els = null;\r
+ Vector regions = getHiddenColumns();\r
+ int blockStart = start, blockEnd = end;\r
+ int[] region;\r
+ int hideStart, hideEnd,w=0;\r
+\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if (hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ blockStart = Math.min(blockStart, hideEnd + 1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+ if (blockStart > blockEnd)\r
+ {\r
+ break;\r
+ }\r
+\r
+ annels.addElement(els = new Annotation[blockEnd-blockStart]);\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+ w+=els.length;\r
+ blockStart = hideEnd + 1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if (end > blockStart)\r
+ {\r
+ annels.addElement(els = new Annotation[end-blockStart+1]);\r
+ if (end-blockStart+1<=alignmentAnnotation.annotations.length)\r
+ {\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+ } else {\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));\r
+ }\r
+ w+=els.length;\r
+ }\r
+ if (w==0)\r
+ return;\r
+ Enumeration e = annels.elements();\r
+ alignmentAnnotation.annotations = new Annotation[w];\r
+ w=0;\r
+ while (e.hasMoreElements())\r
+ {\r
+ Annotation[] chnk = (Annotation[]) e.nextElement();\r
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);\r
+ w+=chnk.length;\r
+ }\r
+ } else {\r
+ alignmentAnnotation.restrict(start, end);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Invert the column selection from first to end-1.\r
+ * leaves hiddenColumns untouched (and unselected)\r
+ * @param first\r
+ * @param end\r
+ */\r
+ public void invertColumnSelection(int first, int width)\r
+ {\r
+ boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;\r
+ for(int i=first; i<width; i++)\r
+ {\r
+ if(contains(i))\r
+ {\r
+ removeElement(i);\r
+ }\r
+ else\r
+ {\r
+ if (!hasHidden || isVisible(i))\r
+ {\r
+ addElement(i);\r
+ }\r
+ }\r
+ } \r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff