Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 00fcb9c..8b7a4c2 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
 import java.util.Locale;
 
 import jalview.api.AlignExportSettingsI;
@@ -34,11 +38,6 @@ import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.util.Platform;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -159,13 +158,16 @@ public class AppletFormatAdapter
           DataSourceType sourceType, FileFormatI fileFormat)
           throws IOException
   {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-    {
-      this.inFile = selectedFile.getPath();
-    }
-    this.inFile = file;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())
@@ -177,11 +179,16 @@ public class AppletFormatAdapter
                         .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
           // needs a File option
           alignFile = new JmolParser(
-                  selectedFile == null ? inFile : selectedFile, sourceType);
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {
@@ -208,8 +215,8 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + fileFormat
-              + "' reader.\n" + e);
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+              + fileFormat + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -290,8 +297,8 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format
-              + "' reader.\n" + e);
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+              + format + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -417,13 +424,13 @@ public class AppletFormatAdapter
       String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
-        System.err.println("Warning raised when writing as " + format
-                + " : " + afile.getWarningMessage());
+        jalview.bin.Console.errPrintln("Warning raised when writing as "
+                + format + " : " + afile.getWarningMessage());
       }
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '"
+      jalview.bin.Console.errPrintln("Failed to write alignment as a '"
               + format.getName() + "' file\n");
       e.printStackTrace();
     }
@@ -481,7 +488,7 @@ public class AppletFormatAdapter
       {
         try
         {
-          System.out.println("Reading file: " + f);
+          jalview.bin.Console.outPrintln("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
@@ -495,37 +502,39 @@ public class AppletFormatAdapter
           memf += r.totalMemory() - r.freeMemory();
           if (al != null)
           {
-            System.out.println("Alignment contains " + al.getHeight()
-                    + " sequences and " + al.getWidth() + " columns.");
+            jalview.bin.Console.outPrintln("Alignment contains "
+                    + al.getHeight() + " sequences and " + al.getWidth()
+                    + " columns.");
             try
             {
-              System.out.println(new AppletFormatAdapter()
+              jalview.bin.Console.outPrintln(new AppletFormatAdapter()
                       .formatSequences(FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
           else
           {
-            System.out.println("Couldn't read alignment");
+            jalview.bin.Console.outPrintln("Couldn't read alignment");
           }
-          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-          System.out.println(
+          jalview.bin.Console
+                  .outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+          jalview.bin.Console.outPrintln(
                   "Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
-          System.err.println("Exception when dealing with " + i
+          jalview.bin.Console.errPrintln("Exception when dealing with " + i
                   + "'th argument: " + args[i] + "\n" + e);
         }
       }
       else
       {
-        System.err.println("Ignoring argument '" + args[i] + "' (" + i
-                + "'th)- not a readable file.");
+        jalview.bin.Console.errPrintln("Ignoring argument '" + args[i]
+                + "' (" + i + "'th)- not a readable file.");
       }
       i++;
     }
@@ -552,8 +561,9 @@ public class AppletFormatAdapter
     DataSourceType protocol = null;
     if (debug)
     {
-      System.out.println("resolving datasource started with:\n>>file\n"
-              + file + ">>endfile");
+      jalview.bin.Console
+              .outPrintln("resolving datasource started with:\n>>file\n"
+                      + file + ">>endfile");
     }
 
     // This might throw a security exception in certain browsers
@@ -570,7 +580,7 @@ public class AppletFormatAdapter
       }
       if (debug)
       {
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
       }
       if (rtn)
@@ -598,7 +608,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Trying to get contents of resource as " + protocol + ":");
       }
       fp = new FileParse(file, protocol);
@@ -610,14 +620,15 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.out.println("Successful.");
+          jalview.bin.Console.outPrintln("Successful.");
         }
       }
     } catch (Exception e)
     {
       if (debug)
       {
-        System.err.println("Exception when accessing content: " + e);
+        jalview.bin.Console
+                .errPrintln("Exception when accessing content: " + e);
       }
       fp = null;
     }
@@ -625,7 +636,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Accessing as paste.");
+        jalview.bin.Console.outPrintln("Accessing as paste.");
       }
       protocol = DataSourceType.PASTE;
       fp = null;
@@ -638,7 +649,8 @@ public class AppletFormatAdapter
         }
       } catch (Exception e)
       {
-        System.err.println("Failed to access content as paste!");
+        jalview.bin.Console
+                .errPrintln("Failed to access content as paste!");
         e.printStackTrace();
         fp = null;
       }
@@ -660,20 +672,22 @@ public class AppletFormatAdapter
         {
           if (debug)
           {
-            System.out.println("Format not identified. Inaccessible file.");
+            jalview.bin.Console.outPrintln(
+                    "Format not identified. Inaccessible file.");
           }
           return null;
         }
         if (debug)
         {
-          System.out.println("Format identified as " + idformat
+          jalview.bin.Console.outPrintln("Format identified as " + idformat
                   + "and expected as " + format);
         }
         if (idformat.equals(format))
         {
           if (debug)
           {
-            System.out.println("Protocol identified as " + protocol);
+            jalview.bin.Console
+                    .outPrintln("Protocol identified as " + protocol);
           }
           return protocol;
         }
@@ -691,7 +705,8 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.err.println("File deemed not accessible via " + protocol);
+          jalview.bin.Console
+                  .errPrintln("File deemed not accessible via " + protocol);
           e.printStackTrace();
         }
       }