apply jalview code style

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c9c5f6d..70f8f3e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -270,22 +270,22 @@ public class Preferences extends GPreferences
   public void ok_actionPerformed(ActionEvent e)
   {
 
-    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
-            .toString(seqLimit.isSelected()));
-    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
-            .toString(rightAlign.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
-            .toString(fullScreen.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
-            .toString(openoverv.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
-            .toString(annotations.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
-            .toString(conservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
-            .toString(quality.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
-            .toString(identity.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+            Boolean.toString(seqLimit.isSelected()));
+    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+            Boolean.toString(rightAlign.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+            Boolean.toString(fullScreen.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+            Boolean.toString(openoverv.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.toString(annotations.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.toString(conservation.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+            Boolean.toString(quality.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.toString(identity.isSelected()));
 
     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
             .getSelectedItem().toString());
@@ -299,32 +299,32 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
             .getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
-            .toString(idItalics.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
-            .toString(showUnconserved.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
-            .toString(showGroupConsensus.isSelected()));
+    Cache.applicationProperties.setProperty("ID_ITALICS",
+            Boolean.toString(idItalics.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+            Boolean.toString(showUnconserved.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+            Boolean.toString(showGroupConsensus.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
             Boolean.toString(showGroupConservation.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
             Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
-            .toString(showConsensLogo.isSelected()));
-    Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
-            .toString(smoothFont.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
-            .toString(showNpTooltip.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
-            .toString(showDbRefTooltip.isSelected()));
-
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
-            .toString(wrap.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+            Boolean.toString(showConsensLogo.isSelected()));
+    Cache.applicationProperties.setProperty("ANTI_ALIAS",
+            Boolean.toString(smoothFont.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+            Boolean.toString(showNpTooltip.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+            Boolean.toString(showDbRefTooltip.isSelected()));
+
+    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+            Boolean.toString(wrap.isSelected()));
 
     Cache.applicationProperties.setProperty("STARTUP_FILE",
             startupFileTextfield.getText());
-    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
-            .toString(startupCheckbox.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+            Boolean.toString(startupCheckbox.isSelected()));
 
     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
             .getSelectedItem().toString());
@@ -364,16 +364,16 @@ public class Preferences extends GPreferences
       }
       // remove last "|"
       links.setLength(links.length() - 1);
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
-              .toString());
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+              links.toString());
     }
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
 
-    Cache.applicationProperties.setProperty("USE_PROXY", Boolean
-            .toString(useProxy.isSelected()));
+    Cache.applicationProperties.setProperty("USE_PROXY",
+            Boolean.toString(useProxy.isSelected()));
 
     if (proxyServerTB.getText().trim().length() < 1)
     {
@@ -381,8 +381,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_SERVER",
+              proxyServerTB.getText());
     }
 
     if (proxyPortTB.getText().trim().length() < 1)
@@ -391,8 +391,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_PORT",
+              proxyPortTB.getText());
     }
 
     if (useProxy.isSelected())
@@ -405,13 +405,13 @@ public class Preferences extends GPreferences
       System.setProperty("http.proxyHost", "");
       System.setProperty("http.proxyPort", "");
     }
-    Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
-            .isSelected()));
+    Cache.setProperty("VERSION_CHECK",
+            Boolean.toString(versioncheck.isSelected()));
     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
     {
       // default is false - we only set this if the user has actively agreed
-      Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
-              .isSelected()));
+      Cache.setProperty("USAGESTATS",
+              Boolean.toString(usagestats.isSelected()));
     }
     if (!questionnaire.isSelected())
     {
@@ -423,28 +423,28 @@ public class Preferences extends GPreferences
       // by just adding the given line
       Cache.removeProperty("NOQUESTIONNAIRES");
     }
-    Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
-            .toString(blcjv.isSelected()));
-    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
-            .toString(clustaljv.isSelected()));
-    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
-            .toString(fastajv.isSelected()));
-    Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
-            .toString(msfjv.isSelected()));
-    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
-            .toString(pfamjv.isSelected()));
-    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
-            .toString(pileupjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
-            .toString(pirjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
-            .toString(modellerOutput.isSelected()));
+    Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+            Boolean.toString(blcjv.isSelected()));
+    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+            Boolean.toString(clustaljv.isSelected()));
+    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+            Boolean.toString(fastajv.isSelected()));
+    Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+            Boolean.toString(msfjv.isSelected()));
+    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+            Boolean.toString(pfamjv.isSelected()));
+    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+            Boolean.toString(pileupjv.isSelected()));
+    Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+            Boolean.toString(pirjv.isSelected()));
+    Cache.applicationProperties.setProperty("PIR_MODELLER",
+            Boolean.toString(modellerOutput.isSelected()));
     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
-    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
-            .toString(autoCalculateConsCheck.isSelected()));
-    Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
-            .toString(padGaps.isSelected()));
+    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+            Boolean.toString(autoCalculateConsCheck.isSelected()));
+    Cache.applicationProperties.setProperty("PAD_GAPS",
+            Boolean.toString(padGaps.isSelected()));
 
     dasSource.saveProperties(Cache.applicationProperties);
     wsPrefs.updateAndRefreshWsMenuConfig(false);
@@ -462,9 +462,10 @@ public class Preferences extends GPreferences
    */
   public void startupFileTextfield_mouseClicked()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"), new String[]
-    { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[]
+            { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
             new String[]
             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));