minor cleanup

igvteam · Jun 12, 2020 · 1aedd43 · 1aedd43
1 parent f9690c6
commit 1aedd43
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Showing 3 changed files with 2 additions and 72 deletions.
diff --git a/src/main/java/org/broad/igv/sam/AlignmentDataManager.java b/src/main/java/org/broad/igv/sam/AlignmentDataManager.java
@@ -390,7 +390,7 @@ private boolean intervalInView(AlignmentInterval interval) {
 
 
     AlignmentInterval loadInterval(String chr, int start, int end, AlignmentTrack.RenderOptions renderOptions) {
-System.out.println("Load interval");
+
         String sequence = chrMappings.containsKey(chr) ? chrMappings.get(chr) : chr;
 
         DownsampleOptions downsampleOptions = new DownsampleOptions();

diff --git a/src/main/java/org/broad/igv/ui/IGV.java b/src/main/java/org/broad/igv/ui/IGV.java
@@ -2053,7 +2053,7 @@ public class StartupRunnable implements Runnable {
         public void run() {
             final boolean runningBatch = igvArgs.getBatchFile() != null;
             BatchRunner.setIsBatchMode(runningBatch);
-            
+
             UIUtilities.invokeOnEventThread(() -> mainFrame.setIconImage(getIconImage()));
             if (Globals.IS_MAC) {
                 setAppleDockIcon();

diff --git a/src/main/java/org/broad/igv/util/HttpUtils.java b/src/main/java/org/broad/igv/util/HttpUtils.java
@@ -571,76 +571,6 @@ public void actionPerformed(ActionEvent e) {
     }
 
 
-    public void uploadGenomeSpaceFile(String uri, File file, Map<String, String> headers) throws IOException {
-
-        HttpURLConnection urlconnection = null;
-        OutputStream bos = null;
-
-        URL url = HttpUtils.createURL(uri);
-        urlconnection = openConnection(url, headers, "PUT");
-        urlconnection.setDoOutput(true);
-        urlconnection.setDoInput(true);
-
-        bos = new BufferedOutputStream(urlconnection.getOutputStream());
-        BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file));
-        int i;
-        // read byte by byte until end of stream
-        while ((i = bis.read()) > 0) {
-            bos.write(i);
-        }
-        bos.close();
-        int responseCode = urlconnection.getResponseCode();
-
-        // Error messages below.
-        if (responseCode >= 400) {
-            String message = readErrorStream(urlconnection);
-            throw new IOException("Error uploading " + file.getName() + " : " + message);
-        }
-    }
-
-
-    public String createGenomeSpaceDirectory(URL url, String body) throws IOException {
-
-        HttpURLConnection urlconnection = null;
-        OutputStream bos = null;
-
-        Map<String, String> headers = new HashMap<String, String>();
-        headers.put("Content-Type", "application/json");
-        headers.put("Content-Length", String.valueOf(body.getBytes().length));
-
-        urlconnection = openConnection(url, headers, "PUT");
-        urlconnection.setDoOutput(true);
-        urlconnection.setDoInput(true);
-
-        bos = new BufferedOutputStream(urlconnection.getOutputStream());
-        bos.write(body.getBytes());
-        bos.close();
-        int responseCode = urlconnection.getResponseCode();
-
-        // Error messages below.
-        StringBuffer buf = new StringBuffer();
-        InputStream inputStream;
-
-        if (responseCode >= 200 && responseCode < 300) {
-            inputStream = urlconnection.getInputStream();
-        } else {
-            inputStream = urlconnection.getErrorStream();
-        }
-        BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
-        String nextLine;
-        while ((nextLine = br.readLine()) != null) {
-            buf.append(nextLine);
-            buf.append('\n');
-        }
-        inputStream.close();
-
-        if (responseCode >= 200 && responseCode < 300) {
-            return buf.toString();
-        } else {
-            throw new IOException("Error creating GS directory: " + buf.toString());
-        }
-    }
-
     /**
      * Code for disabling SSL certification
      */