formatting

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 7c5223c..d30ed20 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -163,7 +163,7 @@ public class IdentifyFile
         else if (data.indexOf(">") > -1)
         {
           // FASTA, PIR file or BLC file
-          boolean checkPIR = false,starterm=false;
+          boolean checkPIR = false, starterm = false;
           if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
           {
             // watch for PIR file attributes
@@ -184,7 +184,8 @@ public class IdentifyFile
             String data2 = source.nextLine();
             if (checkPIR)
             {
-              starterm = (data1!=null && data1.indexOf("*")>-1) || (data2!=null && data2.indexOf("*")>-1);
+              starterm = (data1 != null && data1.indexOf("*") > -1)
+                      || (data2 != null && data2.indexOf("*") > -1);
             }
             if (data2 != null && data.indexOf("*") > -1)
             {
@@ -200,7 +201,8 @@ public class IdentifyFile
               // TODO : AMSA File is indicated if there is annotation in the
               // FASTA file - but FASTA will automatically generate this at the
               // mo.
-              if (!checkPIR) {
+              if (!checkPIR)
+              {
                 break;
               }
             }
@@ -208,29 +210,37 @@ public class IdentifyFile
           // final check for PIR content. require
           // >P1;title\n<blah>\nterminated sequence to occur at least once.
 
-          // TODO the PIR/fasta ambiguity may be the use case that is needed to have
+          // TODO the PIR/fasta ambiguity may be the use case that is needed to
+          // have
           // a 'Parse as type XXX' parameter for the applet/application.
           if (checkPIR)
           {
-            String dta=null;
+            String dta = null;
             if (!starterm)
             {
-              do {
-                try {
+              do
+              {
+                try
+                {
                   dta = source.nextLine();
-                } catch(IOException ex) {};
-                if (dta!=null && dta.indexOf("*")>-1)
+                } catch (IOException ex)
+                {
+                }
+                ;
+                if (dta != null && dta.indexOf("*") > -1)
                 {
                   starterm = true;
                 }
-              } while (dta!=null && !starterm);
+              } while (dta != null && !starterm);
             }
             if (starterm)
             {
-              reply="PIR";
+              reply = "PIR";
               break;
-            } else {
-              reply="FASTA"; // probably a bad choice!
+            }
+            else
+            {
+              reply = "FASTA"; // probably a bad choice!
             }
           }
           // read as a FASTA (probably)