msalign.patch

Index: src/edu/ucsd/msalign/spec/align7/AlignFasta.java
===================================================================
--- src/edu/ucsd/msalign/spec/align7/AlignFasta.java	(revision 7223)
+++ src/edu/ucsd/msalign/spec/align7/AlignFasta.java	(working copy)
@@ -47,6 +47,7 @@
     /** seqence information */
     ResList resList;
     private ResMassSeq seqs[];
+    private ResMassSeq seqsFull[];
 
     private AlignResult alignResults[][][];
 
@@ -82,6 +83,7 @@
                 seq_list.add(s);
             }
         }
+        seqsFull = seq_list.toArray(new ResMassSeq[0]);
         seqs = seq_list.toArray(new ResMassSeq[0]);
         //doLenStat();
         /* we use b-ions for mass lists of proteins in the database, and convert
@@ -95,6 +97,13 @@
         }
     }
 
+    public void updateSeq(int... proteinIds) {
+        seqs = new ResMassSeq[proteinIds.length];
+        for (int i = 0; i < proteinIds.length; i++) {
+            seqs[i] = seqsFull[proteinIds[i]];
+        }
+        fastFilter = new PtmFastFilter(seqs, mng);
+    }
 
     public void doLenStat() {
         int cnt[] = new int[1000000];