diff --git a/uk/ac/sanger/artemis/editor/Annotation.java b/uk/ac/sanger/artemis/editor/Annotation.java index 90dc3c8c4bca3d6185c9c404f860adb0da6d71aa..161e2ec9f37088bc521f5882caa39c59a9734ec9 100644 --- a/uk/ac/sanger/artemis/editor/Annotation.java +++ b/uk/ac/sanger/artemis/editor/Annotation.java @@ -184,7 +184,7 @@ public class Annotation extends JEditorPane s = getDatabaseHTML(s,"EMBL:"); s = getGeneDBHTML(s); - int ind = s.indexOf("/gene"); +// int ind = s.indexOf("/gene"); Document doc = getDocument(); int offset = doc.getLength(); @@ -394,9 +394,13 @@ public class Annotation extends JEditorPane ind1 = ind2+1; } - // if ortholog then delete gene line as well + // if ortholog then delete gene and product lines as well if(ortholog) - ind2 = txt.indexOf("<br>",ind2+4); + { + ind2 = txt.indexOf("<br>/product="); + if(ind2 > -1) + ind2 = txt.indexOf("<br>",ind2+4); + } if(ind2 == -1 || ind2 > txt.length()) ind2 = txt.length(); diff --git a/uk/ac/sanger/artemis/editor/DataCollectionPane.java b/uk/ac/sanger/artemis/editor/DataCollectionPane.java index c48bcd753429244bb04397d106a88dcbb0d9c690..d5855547a64155bb1f1f6634b9a66cbefb08a637 100644 --- a/uk/ac/sanger/artemis/editor/DataCollectionPane.java +++ b/uk/ac/sanger/artemis/editor/DataCollectionPane.java @@ -468,7 +468,6 @@ public class DataCollectionPane extends JScrollPane { public Object construct() { - final String env[] = { "PATH=/usr/local/pubseq/bin/" }; StringBuffer query = new StringBuffer(); @@ -841,7 +840,10 @@ public class DataCollectionPane extends JScrollPane { String geneName = hit.getGeneName(); if(hit.getGeneName() != null) - orthoText = "<br>\n/gene=\""+hit.getGeneName()+"\""; + orthoText = "<br>\n/gene=\""+hit.getGeneName()+"\""+ + "<br>\n/product=\""+hit.getDescription()+"\""; + else + orthoText = "<br>\n/product=\""+hit.getDescription()+"\""; } // System.out.println("ID "+hit.getID()); diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java index 366c7abee9def9184cb2859a2a6bd191373f148b..d458e60fad6e9dcb2dbdbe8247644d67780b981b 100644 --- a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java +++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java @@ -208,21 +208,14 @@ public class DataViewInternalFrame extends JInternalFrame protected void reReadSelectedResults() { - JSplitPane split = (JSplitPane)tabPane.getSelectedComponent(); + ActiveJSplitPane split = (ActiveJSplitPane)tabPane.getSelectedComponent(); Component comps[] = split.getComponents(); for(int i=0; i<comps.length;i++) { - if(comps[i] instanceof JSplitPane) + if(comps[i] instanceof FastaTextPane) { - Component comps2[] = ((JSplitPane)comps[i]).getComponents(); - for(int j=0; j<comps2.length;j++) - { - if(comps2[j] instanceof FastaTextPane) - { - ((FastaTextPane)comps2[j]).reRead(); - return; - } - } + ((FastaTextPane)comps[i]).reRead(); + return; } } }