JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 009d946..a317106 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -153,7 +153,6 @@ import java.util.Vector;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JFileChooser;
-import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
@@ -1043,9 +1042,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       WsParamSetI set = new HMMERPreset();
-      ParamDatastoreI store = HMMERParamStore.forBuild();
-      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
-              args);
+      ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+      WsJobParameters params = new WsJobParameters(store, set, args);
       if (params.showRunDialog())
       {
         args = params.getJobParams();
@@ -1069,9 +1067,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!withDefaults)
     {
       WsParamSetI set = new HMMERPreset();
-      ParamDatastoreI store = HMMERParamStore.forAlign();
-      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
-              args);
+      ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+      WsJobParameters params = new WsJobParameters(store, set, args);
       if (params.showRunDialog())
       {
         args = params.getJobParams();
@@ -1095,9 +1092,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!withDefaults)
     {
       WsParamSetI set = new HMMERPreset();
-      ParamDatastoreI store = HMMERParamStore.forSearch();
-      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
-              args);
+      ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+      WsJobParameters params = new WsJobParameters(store, set, args);
       if (params.showRunDialog())
       {
         args = params.getJobParams();