diff --git a/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java b/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java index 7d4521b2..dc3dcae6 100644 --- 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 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 index 3e2d4f05..5a5e74d6 100644 --- 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 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 index 3d78ea17..a37d3542 100644 --- 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("Tool versions used in this app
" + + "- Minimap2 v2.17-r974-dirty, commit d2de282

" + + + "- Samtools v1.10, commit 5ca6ee2

" + + + "- F5C v0.3-beta, commit cea05f7")); + 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 index 3f259ab9..2e91cf50 100644 --- 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 index 50f2a457..c8ce1fc9 100755 Binary files a/app/src/main/jniLibs/armeabi-v7a/libminimapshared.so and b/app/src/main/jniLibs/armeabi-v7a/libminimapshared.so differ diff --git a/app/src/main/res/layout/activity_minit.xml b/app/src/main/res/layout/activity_minit.xml index 5d088ed4..e0a91f91 100644 --- 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" /> + +