- * @param fake - don't actually build lists - just get types\r
- * @return\r
- public static Object[] buildXProductsList(boolean dna, SequenceI[] seqs, AlignmentI dataset, boolean fake)\r
- {\r
- String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(\r
- dna, seqs, dataset);\r
- if (types != null)\r
- {\r
- System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));\r
- for (int t = 0; t < types.length; t++)\r
- {\r
- System.out.println("Type: " + types[t]);\r
- SequenceI[] prod = \r
- jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);\r
- System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod!=null)\r
- {\r
- for (int p=0; p<prod.length; p++)\r
- {\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
-\r
- } else {\r
- System.out.println("Trying getProducts for "+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 sequences.\r
- SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
- .getSequencesArray(), dna, null, ds);\r
- System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod!=null)\r
- {\r
- // select non-equivalent sequences from dataset list\r
- for (int p=0; p<prod.length; p++)\r
- {\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
- }\r
- }\r
-\r
- }\r
- }\r
+ * @param fake -\r
+ * don't actually build lists - just get types\r
+ * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]\r
+ * seqs, AlignmentI dataset, boolean fake) { String types[] =\r
+ * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,\r
+ * dataset); if (types != null) { System.out.println("Xref Types for:\r
+ * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {\r
+ * System.out.println("Type: " + types[t]); SequenceI[] prod =\r
+ * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);\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