+/*\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
+ * 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
package jalview.analysis;\r
\r
import java.util.Enumeration;\r
{\r
if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))\r
{\r
- System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");\r
+ System.err\r
+ .println("TODO: unimplemented sequence retrieval for coding region sequence.");\r
// TODO: retrieve CDS dataset sequences\r
// need global dataset sequence retriever/resolver to reuse refs\r
// and construct Mapping entry.\r
xrfs = t;\r
try\r
{\r
- retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element\r
+ retrieved = sftch.getSequences(xrfs); // problem here is we don't\r
+ // know which of xrfs\r
+ // resulted in which\r
+ // retrieved element\r
} catch (Exception e)\r
{\r
System.err\r
for (int rs = 0; rs < retrieved.length; rs++)\r
{\r
// TODO: examine each sequence for 'redundancy'\r
- jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();\r
+ jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]\r
+ .getDBRef();\r
if (dbr != null && dbr.length > 0)\r
{\r
for (int di = 0; di < dbr.length; di++)\r
{\r
- // find any entry where we should put in the sequence being cross-referenced into the map\r
+ // find any entry where we should put in the sequence being\r
+ // cross-referenced into the map\r
jalview.datamodel.Mapping map = dbr[di].getMap();\r
if (map != null)\r
{\r
if (map.getTo() != null && map.getMap() != null)\r
{\r
- // should search the local dataset to find any existing candidates for To !\r
+ // should search the local dataset to find any existing\r
+ // candidates for To !\r
try\r
{\r
- // compare ms with dss and replace with dss in mapping if map is congruent\r
+ // compare ms with dss and replace with dss in mapping\r
+ // if map is congruent\r
SequenceI ms = map.getTo();\r
int sf = map.getMap().getToLowest();\r
int st = map.getMap().getToHighest();\r
SequenceI mappedrg = ms.getSubSequence(sf, st);\r
SequenceI loc = dss.getSubSequence(sf, st);\r
- if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(\r
- loc.getSequenceAsString()))\r
+ if (mappedrg.getLength() > 0\r
+ && mappedrg.getSequenceAsString().equals(\r
+ loc.getSequenceAsString()))\r
{\r
System.err\r
.println("Mapping updated for retrieved crossreference");\r
- // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.\r
+ // method to update all refs of existing To on\r
+ // retrieved sequence with dss and merge any props\r
+ // on To onto dss.\r
map.setTo(dss);\r
}\r
} catch (Exception e)\r
boolean direct, boolean dna)\r
{\r
boolean found = false;\r
- SequenceI[] typer=new SequenceI[1];\r
+ SequenceI[] typer = new SequenceI[1];\r
if (dataset == null)\r
return false;\r
if (dataset.getSequences() == null)\r
{\r
typer[0] = nxt;\r
boolean isDna = jalview.util.Comparison.isNucleotide(typer);\r
- if ((direct && isDna == dna) || (!direct && isDna!=dna))\r
+ if ((direct && isDna == dna) || (!direct && isDna != dna))\r
{\r
// skip this sequence because it is same molecule type\r
continue;\r
* System.out.println("Found " + ((prod == null) ? "no" : "" +\r
* prod.length) + " products"); if (prod!=null) { for (int p=0; p<prod.length;\r
* p++) { System.out.println("Prod "+p+":\r
- * "+prod[p].getDisplayId(true)); } } }\r
- * } else { System.out.println("Trying getProducts for\r
- * "+al.getSequenceAt(0).getDisplayId(true)); System.out.println("Search DS\r
- * Xref for: "+(dna ? "dna" : "prot")); // have a bash at finding the products\r
- * amongst all the retrieved sequences. SequenceI[] prod =\r
- * jalview.analysis.CrossRef.findXrefSequences(al .getSequencesArray(), dna,\r
- * null, ds); System.out.println("Found " + ((prod == null) ? "no" : "" +\r
- * prod.length) + " products"); if (prod!=null) { // select non-equivalent\r
- * sequences from dataset list for (int p=0; p<prod.length; p++) {\r
- * System.out.println("Prod "+p+": "+prod[p].getDisplayId(true)); } }\r
- * } }\r
+ * "+prod[p].getDisplayId(true)); } } } } else {\r
+ * System.out.println("Trying getProducts for\r
+ * "+al.getSequenceAt(0).getDisplayId(true));\r
+ * System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot")); //\r
+ * have a bash at finding the products amongst all the retrieved\r
+ * sequences. SequenceI[] prod =\r
+ * jalview.analysis.CrossRef.findXrefSequences(al\r
+ * .getSequencesArray(), dna, null, ds); System.out.println("Found " +\r
+ * ((prod == null) ? "no" : "" + prod.length) + " products"); if\r
+ * (prod!=null) { // select non-equivalent sequences from dataset list\r
+ * for (int p=0; p<prod.length; p++) { System.out.println("Prod\r
+ * "+p+": "+prod[p].getDisplayId(true)); } } } }\r
*/\r
-}
\ No newline at end of file
+}\r
git://source.jalview.org / jalview.git / blobdiff