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genopri-shcs/project/GenomicPrivacy(android)/GenomicPrivacy/src/FrameWork/Writer.java
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Writer.java
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/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package FrameWork;
import java.io.ByteArrayOutputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.sql.Date;
import android.graphics.Bitmap;
import android.graphics.BitmapFactory;
import android.os.Environment;
import com.example.genomicprivacy.ContextApp;
import com.itextpdf.text.BaseColor;
import com.itextpdf.text.Document;
import com.itextpdf.text.Element;
import com.itextpdf.text.Font;
import com.itextpdf.text.FontFactory;
import com.itextpdf.text.Image;
import com.itextpdf.text.PageSize;
import com.itextpdf.text.Paragraph;
import com.itextpdf.text.Phrase;
import com.itextpdf.text.Rectangle;
import com.itextpdf.text.pdf.PdfPCell;
import com.itextpdf.text.pdf.PdfPTable;
import com.itextpdf.text.pdf.PdfWriter;
// TODO: Auto-generated Javadoc
/**
* The Class Writer. This write the pdf into a file
*
* @author raisaro
*/
public class Writer {
/** The path output file. */
String pathOutputFile;
/** The document. */
Document document;
/**
* Instantiates a new writer.
*
* @param path the path
*/
public Writer(String path){
pathOutputFile = path;
document = new Document(PageSize.A4, 25, 25, 50, 50);
}
/**
* Generate pdf report.
*
* @param predictions the predictions
* @param traits the traits
* @param group the group
* @param ID_p the patient ID
* @throws Exception the exception
*/
public void generatePDFreport (String[] predictions,String[] traits,String[] group, int ID_p) throws Exception{
PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(pathOutputFile));
document.open();
Image logo;
try {
// get input stream
InputStream ims = ContextApp.getContext().getAssets().open("icon.jpg");
Bitmap bmp = BitmapFactory.decodeStream(ims);
ByteArrayOutputStream stream = new ByteArrayOutputStream();
bmp.compress(Bitmap.CompressFormat.PNG, 100, stream);
logo = Image.getInstance(stream.toByteArray());
}
catch(IOException ex) {
return;
}
logo.scalePercent(30f);
float[] columnWidths1 = {0.2f, 0.8f};
PdfPTable table_title = new PdfPTable(columnWidths1);
PdfPCell c01 = new PdfPCell(logo, false);
PdfPCell c02 = new PdfPCell(new Paragraph("HIV Pharmacogenomic report | Project #693 | Patient "+ID_p,
FontFactory.getFont(FontFactory.HELVETICA, 20, Font.BOLD, BaseColor.BLACK)));
c01.setVerticalAlignment(Element.ALIGN_MIDDLE);
c02.setVerticalAlignment(Element.ALIGN_MIDDLE);
c01.setBorder(Rectangle.NO_BORDER);
c02.setBorder(Rectangle.NO_BORDER);
table_title.addCell(c01);
table_title.addCell(c02);
table_title.setWidthPercentage(100);
table_title.setSpacingBefore(0);
table_title.setSpacingAfter(25);
document.add(table_title);
//----------------------------------------------------------------------------------
PdfPTable table1 = new PdfPTable(1);
table1.setWidthPercentage(100);
PdfPCell c11 = new PdfPCell(new Phrase("These data are exclusively provided in the frame of an "
+ "investigational project. Clinically relevant results need to be confirmed by an accredited "
+ "clinical laboratory.\nThese data reveal the genetic component of the described traits. "
+ "Environmental, viral and other factors are to be considered for the correct interpretation "
+ "of individual risk.",FontFactory.getFont(FontFactory.HELVETICA, 10, Font.NORMAL, BaseColor.BLACK)));
c11.setLeading(1.5f, 1.5f);
c11.setPaddingBottom(8);
table1.addCell(c11);
document.add(table1);
//----------------------------------------------------------------------------------
PdfPTable table2 = new PdfPTable(2);
table2.setSpacingBefore(20);
table2.setSpacingAfter(20);
table2.setWidthPercentage(100);
PdfPCell c21 = new PdfPCell(new Phrase("SHCS ID",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c21.setPaddingTop(15);
c21.setPaddingBottom(15);
c21.setBorderColor(BaseColor.GRAY);
PdfPCell c22 = new PdfPCell(new Phrase("SHCS_" + ID_p,
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c22.setPaddingTop(15);
c22.setPaddingBottom(15);
c22.setBorderColor(BaseColor.GRAY);
PdfPCell c23 = new PdfPCell(new Phrase("Test order date:",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.NORMAL, BaseColor.BLACK)));
c23.setPaddingBottom(5);
c23.setBorderColor(BaseColor.GRAY);
Date d1 = new Date(System.currentTimeMillis());
PdfPCell c24 = new PdfPCell(new Phrase(d1.toString(),
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.NORMAL, BaseColor.BLACK)));
c24.setPaddingBottom(5);
c24.setBorderColor(BaseColor.GRAY);
PdfPCell c25 = new PdfPCell(new Phrase("Test run date:",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.NORMAL, BaseColor.BLACK)));
c25.setPaddingBottom(5);
c25.setBorderColor(BaseColor.GRAY);
PdfPCell c26 = new PdfPCell(new Phrase(d1.toString(),
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.NORMAL, BaseColor.BLACK)));
c26.setPaddingBottom(5);
c26.setBorderColor(BaseColor.GRAY);
table2.addCell(c21);
table2.addCell(c22);
table2.addCell(c23);
table2.addCell(c24);
table2.addCell(c25);
table2.addCell(c26);
document.add(table2);
//----------------------------------------------------------------------------------
float[] colomnWidths3 = {0.2f,0.35f,0.40f};
PdfPTable table3 = new PdfPTable(colomnWidths3);
table3.setWidthPercentage(100);
table3.setSpacingAfter(20);
PdfPCell c31 = new PdfPCell(new Phrase("Group",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c31.setPaddingTop(5);
c31.setPaddingBottom(5);
c31.setBorderColor(BaseColor.GRAY);
PdfPCell c32 = new PdfPCell(new Phrase("Trait",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c32.setPaddingTop(5);
c32.setPaddingBottom(5);
c32.setBorderColor(BaseColor.GRAY);
PdfPCell c33 = new PdfPCell(new Phrase("Prediction",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c33.setPaddingTop(5);
c33.setPaddingBottom(5);
c33.setBorderColor(BaseColor.GRAY);
table3.addCell(c31);
table3.addCell(c32);
table3.addCell(c33);
Font f = FontFactory.getFont(FontFactory.HELVETICA, 9, Font.NORMAL, BaseColor.BLACK);
String previousGroup = "";
for(int i=0; i<traits.length;i++){
PdfPCell c3a;
if(!group[i].equals(previousGroup)){
c3a = new PdfPCell(new Phrase(group[i]));
previousGroup = group[i];
}else{
c3a = new PdfPCell();
}
if(predictions[i] != null){
PdfPCell c3b = new PdfPCell(new Phrase(traits[i],f));
PdfPCell c3c = new PdfPCell(new Phrase(predictions[i],f));
c3a.setPaddingBottom(5);
c3a.setLeading(1f, 1f);
c3b.setPaddingBottom(5);
c3b.setLeading(1f, 1f);
c3c.setPaddingBottom(5);
c3c.setLeading(1f, 1f);
c3a.setBorder(Rectangle.LEFT);
if(!group[i].equals(previousGroup)){
c3a.enableBorderSide(Rectangle.BOTTOM);
}
table3.addCell(c3a);
table3.addCell(c3b);
table3.addCell(c3c);
}
}
document.add(table3);
//----------------------------------------------------------------------------------
float[] colomnWidths4 = {0.20f,0.30f,0.50f};
PdfPTable table4 = new PdfPTable(colomnWidths4);
table4.setWidthPercentage(100);
PdfPCell c41 = new PdfPCell(new Phrase("HLA Gene",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c41.setPaddingTop(5);
c41.setPaddingBottom(5);
c41.setBorderColor(BaseColor.GRAY);
PdfPCell c42 = new PdfPCell(new Phrase("Predicted allele 1",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c42.setPaddingTop(5);
c42.setPaddingBottom(5);
c42.setBorderColor(BaseColor.GRAY);
PdfPCell c43 = new PdfPCell(new Phrase("Predicted allele 2",
FontFactory.getFont(FontFactory.HELVETICA, 10, Font.BOLD, BaseColor.BLACK)));
c43.setPaddingTop(5);
c43.setPaddingBottom(5);
c43.setBorderColor(BaseColor.GRAY);
PdfPCell c44 = new PdfPCell(new Phrase("A",f));
c44.setPaddingTop(5);
c44.setPaddingBottom(5);
c44.setBorderColor(BaseColor.GRAY);
PdfPCell c45 = new PdfPCell(new Phrase("Prediction not available",f));
c45.setPaddingTop(5);
c45.setPaddingBottom(5);
c45.setBorderColor(BaseColor.GRAY);
PdfPCell c46 = new PdfPCell(new Phrase("Prediction not available",f));
c46.setPaddingTop(5);
c46.setPaddingBottom(5);
c46.setBorderColor(BaseColor.GRAY);
PdfPCell c47 = new PdfPCell(new Phrase("B",f));
c47.setPaddingTop(5);
c47.setPaddingBottom(5);
c47.setBorderColor(BaseColor.GRAY);
PdfPCell c48 = new PdfPCell(new Phrase("Prediction not available",f));
c48.setPaddingTop(5);
c48.setPaddingBottom(5);
c48.setBorderColor(BaseColor.GRAY);
PdfPCell c49 = new PdfPCell(new Phrase("Prediction not available",f));
c49.setPaddingTop(5);
c49.setPaddingBottom(5);
c49.setBorderColor(BaseColor.GRAY);
PdfPCell c410 = new PdfPCell(new Phrase("C",f));
c410.setPaddingTop(5);
c410.setPaddingBottom(5);
c410.setBorderColor(BaseColor.GRAY);
PdfPCell c411 = new PdfPCell(new Phrase("Prediction not available",f));
c411.setPaddingTop(5);
c411.setPaddingBottom(5);
c411.setBorderColor(BaseColor.GRAY);
PdfPCell c412 = new PdfPCell(new Phrase("Prediction not available",f));
c412.setPaddingTop(5);
c412.setPaddingBottom(5);
c412.setBorderColor(BaseColor.GRAY);
table4.addCell(c41);
table4.addCell(c42);
table4.addCell(c43);
table4.addCell(c44);
table4.addCell(c45);
table4.addCell(c46);
table4.addCell(c47);
table4.addCell(c48);
table4.addCell(c49);
table4.addCell(c410);
table4.addCell(c411);
table4.addCell(c412);
document.add(table4);
document.close();
}
}
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