JAL-4159 fix sense of console/alignment output suppression flags and make sure all...

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6800b0c..fb89355 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -158,16 +158,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     float[][] alignmentScores = new float[seqs.length][seqs.length];
     double totscore = 0D;
     int count = seqs.length;
-    suppressTextbox = count<10;
-    discardAlignments = count<15;
+    suppressTextbox = count>10;
+    discardAlignments = count>15;
     boolean first = true;
 
     progress = 0;
     firePropertyChange(TOTAL, 0, total);
 
-    suppressTextbox = count<10;
-    discardAlignments = count<15;
-
     for (int i = 1; i < count; i++)
     {
       // fill diagonal alignmentScores with Float.NaN
@@ -193,25 +190,25 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
         as.scoreAlignment();
 
-        if (!first)
+        if (!first && !suppressTextbox)
         {
           jalview.bin.Console.outPrintln(DASHES);
           textarea.append(DASHES);
           sb.append(DASHES);
         }
         first = false;
-        if (discardAlignments) {
+        if (!discardAlignments) {
           as.printAlignment(System.out);
         }
         scores[i][j] = as.getMaxScore() / as.getASeq1().length;
         alignmentScores[i][j] = as.getAlignmentScore();
         totscore = totscore + scores[i][j];
-        if (suppressTextbox)
+        if (!suppressTextbox)
         {
           textarea.append(as.getOutput());
           sb.append(as.getOutput());
         }
-        if (discardAlignments)
+        if (!discardAlignments)
         {
           sequences.add(as.getAlignedSeq1());
           sequences.add(as.getAlignedSeq2());