Merge pull request #133 from SanojPunchihewa/bug-fixes

Bug fixes
SanojPunchihewa · Mar 5, 2020 · b478b9b · b478b9b
2 parents 0f1f344 + 8023a89
commit b478b9b
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Showing 7 changed files with 106 additions and 3 deletions.
diff --git a/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java b/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java
@@ -181,6 +181,9 @@ private static ArrayList<Argument> configureArguments(Context context, PipelineS
             case F5C_EVENT_ALIGNMENT:
                 rawFile = R.raw.f5c_event_align_arguments;
                 break;
+            case F5C_METH_FREQ:
+                rawFile = R.raw.f5c_meth_freq_arguments;
+                break;
             default:
                 Log.e(TAG, "Invalid Pipeline Step");
                 break;

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java
@@ -14,6 +14,7 @@
 import android.view.View.OnClickListener;
 import android.view.ViewGroup;
 import android.widget.Button;
+import android.widget.Chronometer;
 import android.widget.LinearLayout;
 import android.widget.LinearLayout.LayoutParams;
 import android.widget.ProgressBar;
@@ -61,6 +62,8 @@ public class ConfirmationActivity extends AppCompatActivity {
 
     Button btnWriteLog;
 
+    Chronometer txtTimer;
+
     Button btnProceed;
 
     Button btnSendResults;
@@ -119,11 +122,34 @@ protected void onCreate(@Nullable final Bundle savedInstanceState) {
             folderPath = getIntent().getExtras().getString("FOLDER_PATH");
         }
 
+        LinearLayout.LayoutParams layoutParams1 =
+                new LinearLayout.LayoutParams(LayoutParams.MATCH_PARENT,
+                        LayoutParams.WRAP_CONTENT);
+        LinearLayout horizontalLayout = new LinearLayout(this);
+        horizontalLayout.setOrientation(LinearLayout.HORIZONTAL);
+
         btnProceed = new Button(this);
+        layoutParams1.weight = 1f;
+        btnProceed.setLayoutParams(layoutParams1);
+        horizontalLayout.addView(btnProceed);
+
+        LinearLayout.LayoutParams layoutParams2 =
+                new LinearLayout.LayoutParams(LayoutParams.MATCH_PARENT,
+                        LayoutParams.WRAP_CONTENT);
+
+        txtTimer = new Chronometer(this);
+        txtTimer.setPadding(20, 0, 0, 0);
+        layoutParams2.weight = 4f;
+        txtTimer.setLayoutParams(layoutParams2);
+        horizontalLayout.addView(txtTimer);
+
+        linearLayout.addView(horizontalLayout);
+
         btnProceed.setText("Run the Pipeline");
         btnProceed.setOnClickListener(new OnClickListener() {
             @Override
             public void onClick(final View v) {
+                txtTimer.start();
                 btnProceed.setEnabled(false);
                 mProgressBar.setVisibility(View.VISIBLE);
                 GUIConfiguration.createPipeline();
@@ -173,7 +199,6 @@ public void run() {
                 new RunPipeline().executeOnExecutor(AsyncTask.THREAD_POOL_EXECUTOR);
             }
         });
-        linearLayout.addView(btnProceed);
 
         mProgressBar = new ProgressBar(this,
                 null,
@@ -272,6 +297,7 @@ protected void onProgressUpdate(final Integer... values) {
         @Override
         protected void onPostExecute(final String s) {
             super.onPostExecute(s);
+            txtTimer.stop();
             GUIConfiguration.setPipelineState(PipelineState.COMPLETED);
             NativeCommands.getNativeInstance().finishPipeline(logPipePath);
             List<PipelineComponent> pipelineComponents = GUIConfiguration.getPipeline();

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/HelpActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/HelpActivity.java
@@ -5,6 +5,7 @@
 import android.net.Uri;
 import android.os.Bundle;
 import android.text.Html;
+import android.text.method.LinkMovementMethod;
 import android.view.View;
 import android.view.View.OnClickListener;
 import android.widget.Button;
@@ -67,6 +68,17 @@ public void onClick(final View v) {
         });
         linearLayout.addView(btnTutorial);
 
+        TextView txtToolVersions = new TextView(this);
+        txtToolVersions.setMovementMethod(LinkMovementMethod.getInstance());
+        txtToolVersions.setText(
+                Html.fromHtml("<b>Tool versions used in this app</b><br>" +
+                        "- Minimap2 v2.17-r974-dirty, commit <a href=\"https://github.com/lh3/minimap2/compare/d2de282...master\">d2de282</a><br><br>"
+                        +
+                        "- Samtools v1.10, commit <a href=\"https://github.com/samtools/samtools/compare/5ca6ee2...develop\">5ca6ee2</a><br><br>"
+                        +
+                        "- F5C v0.3-beta, commit <a href=\"https://github.com/hasindu2008/f5c/compare/cea05f7...master\">cea05f7</a>"));
+        linearLayout.addView(txtToolVersions);
+
         TextView txtContribute = new TextView(this);
         txtContribute.setText(
                 "\nPlease contribute to our work by testing,debugging, developing and submitting issues on our product\n");

diff --git a/app/src/main/java/com/mobilegenomics/f5n/core/PipelineStep.java b/app/src/main/java/com/mobilegenomics/f5n/core/PipelineStep.java
@@ -6,7 +6,8 @@ public enum PipelineStep {
     SAMTOOL_INDEX(2, "samtool index"),
     F5C_INDEX(3, "f5c index"),
     F5C_CALL_METHYLATION(4, "f5c call-methylation"),
-    F5C_EVENT_ALIGNMENT(5, "f5c eventalign");
+    F5C_EVENT_ALIGNMENT(5, "f5c eventalign"),
+    F5C_METH_FREQ(6, "f5c meth-freq");
 
     private final int value;
 

diff --git a/app/src/main/jniLibs/armeabi-v7a/libminimapshared.so b/app/src/main/jniLibs/armeabi-v7a/libminimapshared.so
diff --git a/app/src/main/res/layout/activity_minit.xml b/app/src/main/res/layout/activity_minit.xml
@@ -119,11 +119,20 @@
             android:orientation="vertical" />
     </ScrollView>
 
+    <TextView
+        android:id="@+id/txt_uder_dev"
+        android:text="This option is under development"
+        android:layout_alignParentBottom="true"
+        android:gravity="center_horizontal"
+        android:padding="5dp"
+        android:layout_width="match_parent"
+        android:layout_height="wrap_content" />
+
     <Button
         android:id="@+id/btn_process_job"
         android:layout_width="wrap_content"
         android:layout_height="wrap_content"
-        android:layout_alignParentBottom="true"
+        android:layout_above="@id/txt_uder_dev"
         android:layout_centerHorizontal="true"
         android:layout_marginBottom="10dp"
         android:visibility="gone"

diff --git a/app/src/main/res/raw/f5c_meth_freq_arguments.json b/app/src/main/res/raw/f5c_meth_freq_arguments.json
@@ -0,0 +1,52 @@
+{
+  "args": [
+    {
+      "argName": "Input meth file",
+      "argValue": null,
+      "argDescription": "Call methylation file",
+      "flag": "-i",
+      "argID": "F5C_METH_FREQ_INPUT_FILE",
+      "isDependentOn": "F5C_METH_OUTPUT_FILE",
+      "hasFlag": true,
+      "flagOnly": false,
+      "required": true,
+      "isFile": true
+    },
+    {
+      "argName": "meth freq file",
+      "argValue": null,
+      "argDescription": "Methylation frequency file",
+      "flag": "-o",
+      "argID": "F5C_METH_FREQ_FILE",
+      "isDependentOn": "argIDofanotherArg",
+      "hasFlag": true,
+      "flagOnly": false,
+      "required": true,
+      "isFile": true
+    },
+    {
+      "argName": "Call threshold",
+      "argValue": "2.5",
+      "argDescription": "Call threshold [2.5]",
+      "flag": "-c",
+      "argID": "tobedecided",
+      "isDependentOn": "argIDofanotherArg",
+      "hasFlag": true,
+      "flagOnly": false,
+      "required": false,
+      "isFile": false
+    },
+    {
+      "argName": "Split groups",
+      "argValue": null,
+      "argDescription": "Split groups",
+      "flag": "-s",
+      "argID": "tobedecided",
+      "isDependentOn": "argIDofanotherArg",
+      "hasFlag": true,
+      "flagOnly": true,
+      "required": false,
+      "isFile": false
+    }
+  ]
+}