+ return true;\r
+ }\r
+ /**\r
+ * returns a subset of the sequenceI seuqences,\r
+ * including only those that contain at least one residue.\r
+ * @param sequences SequenceI[]\r
+ * @return SequenceI[]\r
+ */\r
+ public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences) {\r
+ // Identify first row of alignment with residues for prediction\r
+ boolean ungapped[] = new boolean[sequences.length];\r
+ int msflen=0;\r
+ for (int i=0,j=sequences.length; i<j;i++) {\r
+ String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());\r
+ if (tempseq.length()==0)\r
+ ungapped[i]=false;\r
+ else {\r
+ ungapped[i]=true;\r
+ msflen++;\r
+ }\r
+ }\r
+ if (msflen==0)\r
+ return null; // no minimal set\r
+ // compose minimal set\r
+ SequenceI[] mset = new SequenceI[msflen];\r
+ for (int i=0,j=sequences.length,k=0; i<j;i++) {\r
+ if (ungapped[i])\r
+ mset[k++] = sequences[i];\r
+ }\r
+ ungapped = null;\r
+ return mset;\r