8. A method for generating contextual markups of formatted documents, comprising: a) inputting a document into a system for document analysis, comprising a processor and software configured to a) receive textual documents over an electronic communication network and convert textual documents into image files, identify text in said image files, wherein said text is mapped to the document image using a database comprising text of the document; b) permit a user to add contextual markups to said image files wherein said contextual markups are images or HTML tags that are added to an invisible image that maps exactly onto each image of said image file, and wherein said image file is not modified, c) generate an originality report, wherein said generating said originality report comprises the step of highlighting said sections of said image file identified in the originality report as allegedly containing plagiarized text, wherein said highlighting is glyph aware highlighting that associates glyphs with images using the pixel coordinates of the image, which maps to a text database of said document; and d) display said image file on a display screen, wherein said image file simultaneously displays said contextual markups and said highlights; b) adding contextual markups to said image document; c) generating an originality report and highlighting sections of said image file that allegedly contain plagiarized text using said glyph aware highlighting; and d) displaying said image containing said highlighting and said contextual markups, wherein said glyph aware highlighting and said contextual markups are displayed simultaneously.
8. A method for generating contextual markups of formatted documents, comprising: a) inputting a document into a system for document analysis, comprising a processor and software configured to a) receive textual documents over an electronic communication network and convert textual documents into image files, identify text in said image files, wherein said text is mapped to the document image using a database comprising text of the document; b) permit a user to add contextual markups to said image files wherein said contextual markups are images or HTML tags that are added to an invisible image that maps exactly onto each image of said image file, and wherein said image file is not modified, c) generate an originality report, wherein said generating said originality report comprises the step of highlighting said sections of said image file identified in the originality report as allegedly containing plagiarized text, wherein said highlighting is glyph aware highlighting that associates glyphs with images using the pixel coordinates of the image, which maps to a text database of said document; and d) display said image file on a display screen, wherein said image file simultaneously displays said contextual markups and said highlights; b) adding contextual markups to said image document; c) generating an originality report and highlighting sections of said image file that allegedly contain plagiarized text using said glyph aware highlighting; and d) displaying said image containing said highlighting and said contextual markups, wherein said glyph aware highlighting and said contextual markups are displayed simultaneously. 13. The method of claim 8 , wherein said highlighting scales with zooming.