X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=28381bc4925c2602901fcad0b3fad41c4a4b3a82;hb=bc455f675d56d49d0a0f132809d8117f7ffca5ab;hp=929a871106b9c3c4888212175405efac1d13cc9f;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java index 929a871..28381bc 100644 --- a/src/jalview/appletgui/ExtJmol.java +++ b/src/jalview/appletgui/ExtJmol.java @@ -21,11 +21,11 @@ package jalview.appletgui; import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JalviewJmolBinding; +import jalview.io.DataSourceType; import java.awt.Container; import java.util.ArrayList; @@ -48,12 +48,11 @@ public class ExtJmol extends JalviewJmolBinding private AlignmentPanel ap; - protected ExtJmol(jalview.appletgui.AlignFrame alframe, - PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains, - String protocol) + protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry, + SequenceI[][] seq, DataSourceType protocol) { super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq, - chains, protocol); + protocol); } public ExtJmol(Viewer viewer, AlignmentPanel alignPanel, @@ -64,33 +63,18 @@ public class ExtJmol extends JalviewJmolBinding notifyFileLoaded(null, null, null, null, 0); } + @Override public void updateColours(Object source) { - - // TODO Auto-generated method stub - } + @Override public void showUrl(String arg0) { showUrl(arg0, "jmol"); } @Override - public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) - { - AlignmentPanel ap = (AlignmentPanel) alignment; - if (ap.av.isShowSequenceFeatures()) - { - return ap.getFeatureRenderer(); - } - else - { - return null; - } - } - - @Override public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) { return ((AlignmentPanel) alignment).getSequenceRenderer(); @@ -126,6 +110,7 @@ public class ExtJmol extends JalviewJmolBinding // ignore } + @Override public void selectionChanged(BS arg0) { System.out.println(arg0); @@ -134,8 +119,8 @@ public class ExtJmol extends JalviewJmolBinding @Override public void refreshPdbEntries() { - List pdbe = new ArrayList(); - List fileids = new ArrayList(); + List pdbe = new ArrayList<>(); + List fileids = new ArrayList<>(); SequenceI[] sq = ap.av.getAlignment().getSequencesArray(); for (int s = 0; s < sq.length; s++) { @@ -169,8 +154,8 @@ public class ExtJmol extends JalviewJmolBinding { // This never gets called because we haven't overriden the associated Jmol's // console - System.err - .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole=" + System.err.println( + "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole=" + show); } @@ -178,7 +163,6 @@ public class ExtJmol extends JalviewJmolBinding protected JmolAppConsoleInterface createJmolConsole( Container consolePanel, String buttonsToShow) { - // TODO Auto-generated method stub return null; } @@ -191,16 +175,8 @@ public class ExtJmol extends JalviewJmolBinding } @Override - public void releaseReferences(Object svl) - { - // TODO Auto-generated method stub - - } - - @Override public Map getJSpecViewProperty(String arg0) { - // TODO Auto-generated method stub return null; }