/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
+ * This file is part of Jalview.\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
+ * 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 of the License, or (at your option) any later version.\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
+ * 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 along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.analysis;\r
\r
* @param annotations\r
* @param aWidth\r
* @param dataset\r
- * destination dataset for translated sequences and mappings\r
+ * destination dataset for translated sequences and mappings\r
* @return\r
*/\r
public static AlignmentI CdnaTranslate(SequenceI[] selection,\r
* \r
* @param selection\r
* @param seqstring\r
- * @param product -\r
- * array of DbRefEntry objects from which exon map in seqstring\r
- * is derived\r
+ * @param product\r
+ * - array of DbRefEntry objects from which exon map in seqstring is\r
+ * derived\r
* @param viscontigs\r
* @param gapCharacter\r
* @param annotations\r
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],\r
viscontigs, codons, gapCharacter,\r
(product != null) ? product[s] : null); // possibly anonymous\r
- // product\r
+ // product\r
if (newseq != null)\r
{\r
pepseqs.addElement(newseq);\r
* @param viscontigs\r
* @param gapCharacter\r
* @param dataset\r
- * destination dataset for translated sequences\r
+ * destination dataset for translated sequences\r
* @param annotations\r
* @param aWidth\r
* @return\r
{\r
// Have a look at all the codon positions for annotation and put the first\r
// one found into the translated annotation pos.\r
+ int contrib = 0;\r
+ Annotation annot = null;\r
for (int p = 0; p < 3; p++)\r
{\r
if (annotations[is[p]] != null)\r
{\r
- return new Annotation(annotations[is[p]]);\r
+ if (annot == null)\r
+ {\r
+ annot = new Annotation(annotations[is[p]]);\r
+ contrib = 1;\r
+ }\r
+ else\r
+ {\r
+ // merge with last\r
+ Annotation cpy = new Annotation(annotations[is[p]]);\r
+ if (annot.colour == null)\r
+ {\r
+ annot.colour = cpy.colour;\r
+ }\r
+ if (annot.description == null || annot.description.length() == 0)\r
+ {\r
+ annot.description = cpy.description;\r
+ }\r
+ if (annot.displayCharacter == null)\r
+ {\r
+ annot.displayCharacter = cpy.displayCharacter;\r
+ }\r
+ if (annot.secondaryStructure == 0)\r
+ {\r
+ annot.secondaryStructure = cpy.secondaryStructure;\r
+ }\r
+ annot.value += cpy.value;\r
+ contrib++;\r
+ }\r
}\r
}\r
- return null;\r
+ if (contrib > 1)\r
+ {\r
+ annot.value /= (float) contrib;\r
+ }\r
+ return annot;\r
}\r
\r
/**\r
* Translate a na sequence\r
* \r
* @param selection\r
- * sequence displayed under viscontigs visible columns\r
+ * sequence displayed under viscontigs visible columns\r
* @param seqstring\r
- * ORF read in some global alignment reference frame\r
+ * ORF read in some global alignment reference frame\r
* @param viscontigs\r
- * mapping from global reference frame to visible seqstring ORF\r
- * read\r
+ * mapping from global reference frame to visible seqstring ORF read\r
* @param codons\r
- * Definition of global ORF alignment reference frame\r
+ * Definition of global ORF alignment reference frame\r
* @param gapCharacter\r
* @param newSeq\r
* @return sequence ready to be added to alignment.\r
}\r
if (aspos >= codons.aaWidth)\r
{\r
- // update maximum alignment width \r
- // (we can do this without calling checkCodonFrameWidth because it was already done above)\r
+ // update maximum alignment width\r
+ // (we can do this without calling checkCodonFrameWidth because it was\r
+ // already done above)\r
codons.setAaWidth(aspos);\r
}\r
// ready for next translated reading frame alignment position (if any)\r
}\r
if (resSize > 0)\r
{\r
- SequenceI newseq = new Sequence(selection.getName(), protein\r
- .toString());\r
+ SequenceI newseq = new Sequence(selection.getName(),\r
+ protein.toString());\r
if (rf != 0)\r
{\r
jalview.bin.Cache.log\r
* new ranges to exclude untranslated regions. if (skip.size()>0) {\r
* Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {\r
* narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =\r
- * 0; while (sint<skip.size()) { skipint = (int[])\r
- * skip.elementAt(sint); do { iv = (int[]) narange.elementAt(vc); if\r
- * (iv[0]>=skipint[0] && iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { //\r
- * delete beginning of range } else { // truncate range and create new\r
- * one if necessary iv = (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { //\r
- * truncate range iv[0] = skipint[1]; } else {\r
- * } } } else if (iv[0]<skipint[0]) { iv = (int[])\r
- * narange.elementAt(vc+1); } } while (iv[0]) } }\r
+ * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);\r
+ * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&\r
+ * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of\r
+ * range } else { // truncate range and create new one if necessary iv =\r
+ * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate\r
+ * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {\r
+ * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }\r
*/\r
MapList map = new MapList(scontigs, new int[]\r
{ 1, resSize }, 3, 1);\r
}\r
}\r
// register the mapping somehow\r
- // \r
+ //\r
return null;\r
}\r
\r
* @param pep\r
* @param map\r
* @param featureTypes\r
- * hash who's keys are the displayed feature type strings\r
+ * hash who's keys are the displayed feature type strings\r
* @param featureGroups\r
- * hash where keys are feature groups and values are Boolean\r
- * objects indicating if they are displayed.\r
+ * hash where keys are feature groups and values are Boolean objects\r
+ * indicating if they are displayed.\r
*/\r
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,\r
MapList map, Hashtable featureTypes, Hashtable featureGroups)\r
fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups\r
.get(sf[f].featureGroup));\r
if ((featureTypes == null || featureTypes.containsKey(sf[f]\r
- .getType()))\r
- && (fgstate == null || fgstate.booleanValue()))\r
+ .getType())) && (fgstate == null || fgstate.booleanValue()))\r
{\r
if (FeatureProperties.isCodingFeature(null, sf[f].getType()))\r
{\r
git://source.jalview.org / jalview.git / blobdiff